Source: https://github.com/markziemann/shoulder-instability-osteroarthritis
What is the relationship between metabolic syndrome (visceral obesity, hypertension, elevated fasting glucose, and dyslipidaemia) and the transcriptomic profile of shoulder OA when comparing bone biopsies between patients with cuff arthropathy and primary osteoarthritis? For the above analyses to be effective, we will need to adjust for age, sex and CRP. Patients are classified as having metabolic syndrome = YES, or not = No, giving us a discrete variable which takes into account BMI, Fasting glucose, Cholesterol and Blood pressure in accordance with the international diabetes federation definition.
Also I will conduct a comparison of cuff arth to primary OA control for age sex and CRP.
Packages.
suppressPackageStartupMessages({
library(R.utils)
library("zoo")
library("tidyverse")
library("reshape2")
library("DESeq2")
library("gplots")
library("fgsea")
library("MASS")
library("mitch")
library("eulerr")
library("limma")
library("topconfects")
library("kableExtra")
})
Functions.
maplot <- function(de,contrast_name) {
sig <-subset(de, padj < 0.05 )
up <-rownames(subset(de, padj < 0.05 & log2FoldChange > 0))
dn <-rownames(subset(de, padj < 0.05 & log2FoldChange < 0))
GENESUP <- length(up)
GENESDN <- length(dn)
DET=nrow(de)
SUBHEADER = paste(GENESUP, "up, ", GENESDN, "down", DET, "detected")
ns <-subset(de, padj > 0.05 )
plot(log2(de$baseMean),de$log2FoldChange,
xlab="log2 basemean", ylab="log2 foldchange",
pch=19, cex=0.5, col="dark gray",
main=contrast_name, cex.main=1)
points(log2(sig$baseMean),sig$log2FoldChange,
pch=19, cex=0.5, col="red")
mtext(SUBHEADER,cex = 1)
}
make_volcano <- function(de,name) {
sig <- subset(de,padj<0.05)
N_SIG=nrow(sig)
N_UP=nrow(subset(sig,log2FoldChange>0))
N_DN=nrow(subset(sig,log2FoldChange<0))
DET=nrow(de)
HEADER=paste(N_SIG,"@5%FDR,", N_UP, "up", N_DN, "dn", DET, "detected")
plot(de$log2FoldChange,-log10(de$pval),cex=0.5,pch=19,col="darkgray",
main=name, xlab="log2 FC", ylab="-log10 pval")
mtext(HEADER)
grid()
points(sig$log2FoldChange,-log10(sig$pval),cex=0.5,pch=19,col="red")
}
make_heatmap <- function(de,name,groups,mx,n=30){
colfunc <- colorRampPalette(c("blue", "white", "red"))
values <- groups
f <- colorRamp(c("yellow", "orange"))
rr <- range(values)
svals <- (values-rr[1])/diff(rr)
colcols <- rgb(f(svals)/255)
mxn <- mx/rowSums(mx)*1000000
x <- mxn[which(rownames(mxn) %in% rownames(head(de,n))),]
heatmap.2(as.matrix(x),trace="none",col=colfunc(25),scale="row", margins = c(10,15), cexRow=0.5,
main=paste("Top ranked",n,"genes in",name) , ColSideColors = colcols )
}
ss <- read.table("pheno_data.tsv",header=TRUE)
rownames(ss) <- sapply(strsplit(ss$fastq,"_R1_"),"[[",1)
rownames(ss) <- gsub("_L001","",rownames(ss))
rownames(ss) <- gsub("-",".",rownames(ss))
ss <- ss[order(rownames(ss)),]
ss %>%
kbl(caption = "sample sheet") %>%
kable_paper("hover", full_width = F)
Participant_ID | Case | Redcap_ID | Tissue | fastq | pvt.pub | Age | Sex | Primary_OA | Cuff_Arthropathy | Prosthesis | Affected_Side | Height_cm | Weight_kg | BMI | ASA | Smoking | Diabetes | Hypercholesterolaemia | Hypertension | Thyroid | CRP | Creat | eGFR | Urea | Fast_Glucose | hba1c | Metabolic_Syndrome | Tendon_integrity_2_years_post.op | ASES_2_years_post.op_Pain | ASES_2_years_post.op_ADL | ASES_2_years_post.op_Total | Oxford_Baseline | Oxford_3_month | Oxford_12_month | Oxford_24_month | QuickDASH_ | QuickDASH_3_month | QuickDASH_12_month | QuickDASH_24_month | EQ.5D.3L_Baseline | EQ.5D.3L_3_month | EQ.5D.3L_12_month | EQ.5D.3L_24_month | EQVAS_Baseline | EQVAS_3_month | EQVAS_12_month | EQVAS_24_month | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1.1_S41 | AD-CAB_3001 | RC | 53 | capsule | 1-1_S41_L001_R1_001.fastq.gz | NA | 67 | M | NA | NA | NA | Left | 177.80 | 120.0 | 37.90 | 2 | Ever_smoker | No | Yes | Yes | No | 2.9 | 83 | 84 | 7.0 | 5.2 | 5.6 | Yes | Torn | NA | NA | NA | 25 | 41 | 46 | NA | 38.6 | 13.6 | 13.6 | NA | 11222 | 11123 | 21222 | NA | 90 | 50 | 60 | NA |
1.2_S67 | AD-CAB_3001 | RC | 53 | tendon | 1-2_S67_L001_R1_001.fastq.gz | NA | 67 | M | NA | NA | NA | Left | 177.80 | 120.0 | 37.90 | 2 | Ever_smoker | No | Yes | Yes | No | 2.9 | 83 | 84 | 7.0 | 5.2 | 5.6 | Yes | Torn | NA | NA | NA | 25 | 41 | 46 | NA | 38.6 | 13.6 | 13.6 | NA | 11222 | 11123 | 21222 | NA | 90 | 50 | 60 | NA |
1.3_S93 | AD-CAB_3001 | RC | 53 | tear | 1-3_S93_L001_R1_001.fastq.gz | NA | 67 | M | NA | NA | NA | Left | 177.80 | 120.0 | 37.90 | 2 | Ever_smoker | No | Yes | Yes | No | 2.9 | 83 | 84 | 7.0 | 5.2 | 5.6 | Yes | Torn | NA | NA | NA | 25 | 41 | 46 | NA | 38.6 | 13.6 | 13.6 | NA | 11222 | 11123 | 21222 | NA | 90 | 50 | 60 | NA |
10.1_S50 | AD-CAB_3010 | RC | 62 | capsule | 10-1_S50_L001_R1_001.fastq.gz | NA | 58 | M | NA | NA | NA | Left | 179.00 | 98.0 | 30.00 | 2 | Never_smoker | No | No | No | Yes | 2.9 | 82 | 90 | 5.6 | 4.9 | 5.1 | No | Intact | 45 | 17 | 62 | 21 | 45 | 43 | 44 | 45.5 | 4.5 | 11.4 | 20.5 | 11221 | 11111 | 11121 | 11221 | 70 | 70 | 75 | 85 |
10.2_S76 | AD-CAB_3010 | RC | 62 | tendon | 10-2_S76_L001_R1_001.fastq.gz | NA | 58 | M | NA | NA | NA | Left | 179.00 | 98.0 | 30.00 | 2 | Never_smoker | No | No | No | Yes | 2.9 | 82 | 90 | 5.6 | 4.9 | 5.1 | No | Intact | 45 | 17 | 62 | 21 | 45 | 43 | 44 | 45.5 | 4.5 | 11.4 | 20.5 | 11221 | 11111 | 11121 | 11221 | 70 | 70 | 75 | 85 |
10.3_S102 | AD-CAB_3010 | RC | 62 | tear | 10-3_S102_L001_R1_001.fastq.gz | NA | 58 | M | NA | NA | NA | Left | 179.00 | 98.0 | 30.00 | 2 | Never_smoker | No | No | No | Yes | 2.9 | 82 | 90 | 5.6 | 4.9 | 5.1 | No | Intact | 45 | 17 | 62 | 21 | 45 | 43 | 44 | 45.5 | 4.5 | 11.4 | 20.5 | 11221 | 11111 | 11121 | 11221 | 70 | 70 | 75 | 85 |
10B_S21 | AD-CAB_4010 | OA | 90 | bone | 10B_S21_L001_R1_001.fastq.gz | pvt | 80 | F | No | Yes | Reverse | Left | 161.00 | 72.0 | 28.00 | 2 | Never_smoker | No | Yes | No | Yes | 11.2 | 54 | 86 | 8.5 | 7.3 | 5.6 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
10C_S35 | AD-CAB_4010 | OA | 90 | capsule | 10C_S35_L001_R1_001.fastq.gz | pvt | 80 | F | No | Yes | Reverse | Left | 161.00 | 72.0 | 28.00 | 2 | Never_smoker | No | Yes | No | Yes | 11.2 | 54 | 86 | 8.5 | 7.3 | 5.6 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
10S_S49 | AD-CAB_4010 | OA | 90 | synovium | 10S_S49_L001_R1_001.fastq.gz | pvt | 80 | F | No | Yes | Reverse | Left | 161.00 | 72.0 | 28.00 | 2 | Never_smoker | No | Yes | No | Yes | 11.2 | 54 | 86 | 8.5 | 7.3 | 5.6 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
11.1_S51 | AD-CAB_3011 | RC | 63 | capsule | 11-1_S51_L001_R1_001.fastq.gz | NA | 50 | M | NA | NA | NA | Right | 180.00 | 82.0 | 25.00 | 1 | Never_smoker | No | Yes | No | No | 2.9 | 99 | 76 | 6.7 | 5.7 | 6.0 | No | Intact | 35 | 18 | 53 | 18 | 38 | 44 | 46 | 61.4 | 31.8 | 6.8 | 20.5 | 11221 | 11222 | 11111 | 11121 | 75 | 83 | 75 | 78 |
11.2_S77 | AD-CAB_3011 | RC | 63 | tendon | 11-2_S77_L001_R1_001.fastq.gz | NA | 50 | M | NA | NA | NA | Right | 180.00 | 82.0 | 25.00 | 1 | Never_smoker | No | Yes | No | No | 2.9 | 99 | 76 | 6.7 | 5.7 | 6.0 | No | Intact | 35 | 18 | 53 | 18 | 38 | 44 | 46 | 61.4 | 31.8 | 6.8 | 20.5 | 11221 | 11222 | 11111 | 11121 | 75 | 83 | 75 | 78 |
11.3_S103 | AD-CAB_3011 | RC | 63 | tear | 11-3_S103_L001_R1_001.fastq.gz | NA | 50 | M | NA | NA | NA | Right | 180.00 | 82.0 | 25.00 | 1 | Never_smoker | No | Yes | No | No | 2.9 | 99 | 76 | 6.7 | 5.7 | 6.0 | No | Intact | 35 | 18 | 53 | 18 | 38 | 44 | 46 | 61.4 | 31.8 | 6.8 | 20.5 | 11221 | 11222 | 11111 | 11121 | 75 | 83 | 75 | 78 |
11B_S22 | AD-CAB_4011 | OA | 87 | bone | 11B_S22_L001_R1_001.fastq.gz | pub | 76 | M | Yes | No | Reverse | Right | 180.00 | 92.0 | 28.00 | 2 | Never_smoker | No | Yes | Yes | No | 4.0 | 75 | 85 | 7.0 | 6.0 | 6.0 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
11C_S36 | AD-CAB_4011 | OA | 87 | capsule | 11C_S36_L001_R1_001.fastq.gz | pub | 76 | M | No | Yes | Reverse | Right | 180.00 | 92.0 | 28.00 | 2 | Never_smoker | No | Yes | Yes | No | 4.0 | 75 | 85 | 7.0 | 6.0 | 6.0 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
11S_S50 | AD-CAB_4011 | OA | 87 | synovium | 11S_S50_L001_R1_001.fastq.gz | pub | 76 | M | Yes | No | Reverse | Right | 180.00 | 92.0 | 28.00 | 2 | Never_smoker | No | Yes | Yes | No | 4.0 | 75 | 85 | 7.0 | 6.0 | 6.0 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
12.1_S52 | AD-CAB_3012 | RC | 64 | capsule | 12-1_S52_L001_R1_001.fastq.gz | NA | 72 | M | NA | NA | NA | Left | 173.00 | 87.0 | 29.00 | 3 | Never_smoker | Yes | Yes | Yes | No | 2.9 | 108 | 59 | 4.8 | 6.1 | 6.6 | No | NA | 50 | 48 | 98 | 29 | 32 | 48 | 42 | 68.2 | 0.0 | 4.5 | 18.2 | 12221 | 11111 | 11111 | 11111 | 70 | 90 | 80 | 90 |
12.2_S78 | AD-CAB_3012 | RC | 64 | tendon | 12-2_S78_L001_R1_001.fastq.gz | NA | 72 | M | NA | NA | NA | Left | 173.00 | 87.0 | 29.00 | 3 | Never_smoker | Yes | Yes | Yes | No | 2.9 | 108 | 59 | 4.8 | 6.1 | 6.6 | No | NA | 50 | 48 | 98 | 29 | 32 | 48 | 42 | 68.2 | 0.0 | 4.5 | 18.2 | 12221 | 11111 | 11111 | 11111 | 70 | 90 | 80 | 90 |
12.3_S104 | AD-CAB_3012 | RC | 64 | tear | 12-3_S104_L001_R1_001.fastq.gz | NA | 72 | M | NA | NA | NA | Left | 173.00 | 87.0 | 29.00 | 3 | Never_smoker | Yes | Yes | Yes | No | 2.9 | 108 | 59 | 4.8 | 6.1 | 6.6 | No | NA | 50 | 48 | 98 | 29 | 32 | 48 | 42 | 68.2 | 0.0 | 4.5 | 18.2 | 12221 | 11111 | 11111 | 11111 | 70 | 90 | 80 | 90 |
12B_S23 | AD-CAB_4012 | OA | 91 | bone | 12B_S23_L001_R1_001.fastq.gz | pub | 71 | F | Yes | No | Anatomic | Right | 163.00 | 83.0 | 31.00 | 2 | Never_smoker | No | Yes | Yes | No | 2.9 | 73 | 72 | 4.8 | 6.3 | 5.7 | Yes | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
12C_S37 | AD-CAB_4012 | OA | 91 | capsule | 12C_S37_L001_R1_001.fastq.gz | pub | 71 | F | Yes | No | Anatomic | Right | 163.00 | 83.0 | 31.00 | 2 | Never_smoker | No | Yes | Yes | No | 2.9 | 73 | 72 | 4.8 | 6.3 | 5.7 | Yes | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
12S_S51 | AD-CAB_4012 | OA | 91 | synovium | 12S_S51_L001_R1_001.fastq.gz | pub | 71 | F | Yes | No | Anatomic | Right | 163.00 | 83.0 | 31.00 | 2 | Never_smoker | No | Yes | Yes | No | 2.9 | 73 | 72 | 4.8 | 6.3 | 5.7 | Yes | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
13.1_S53 | AD-CAB_3013 | RC | 65 | capsule | 13-1_S53_L001_R1_001.fastq.gz | NA | 68 | F | NA | NA | NA | Right | 161.00 | 104.0 | 40.00 | 3 | Never_smoker | Yes | No | Yes | No | 6.3 | 64 | 86 | 6.8 | 9.2 | 7.1 | Yes | NA | 45 | 45 | 90 | 19 | 34 | 48 | 46 | 75.0 | 50.0 | 6.8 | 2.3 | 11222 | 11221 | 22221 | 21231 | 89 | 78 | 50 | 50 |
13.2_S79 | AD-CAB_3013 | RC | 65 | tendon | 13-2_S79_L001_R1_001.fastq.gz | NA | 68 | F | NA | NA | NA | Right | 161.00 | 104.0 | 40.00 | 3 | Never_smoker | Yes | No | Yes | No | 6.3 | 64 | 86 | 6.8 | 9.2 | 7.1 | Yes | NA | 45 | 45 | 90 | 19 | 34 | 48 | 46 | 75.0 | 50.0 | 6.8 | 2.3 | 11222 | 11221 | 22221 | 21231 | 89 | 78 | 50 | 50 |
13.3_S105 | AD-CAB_3013 | RC | 65 | tear | 13-3_S105_L001_R1_001.fastq.gz | NA | 68 | F | NA | NA | NA | Right | 161.00 | 104.0 | 40.00 | 3 | Never_smoker | Yes | No | Yes | No | 6.3 | 64 | 86 | 6.8 | 9.2 | 7.1 | Yes | NA | 45 | 45 | 90 | 19 | 34 | 48 | 46 | 75.0 | 50.0 | 6.8 | 2.3 | 11222 | 11221 | 22221 | 21231 | 89 | 78 | 50 | 50 |
13B_S24 | AD-CAB_4013 | OA | 89 | bone | 13B_S24_L001_R1_001.fastq.gz | pvt | 69 | F | No | Yes | Reverse | Left | 170.00 | 89.0 | 31.00 | 2 | Never_smoker | No | Yes | Yes | No | 2.9 | 81 | 85 | 5.1 | 5.4 | 5.9 | Yes | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
13C_S38 | AD-CAB_4013 | OA | 89 | capsule | 13C_S38_L001_R1_001.fastq.gz | pvt | 69 | F | No | Yes | Reverse | Left | 170.00 | 89.0 | 31.00 | 2 | Never_smoker | No | Yes | Yes | No | 2.9 | 81 | 85 | 5.1 | 5.4 | 5.9 | Yes | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
13S_S52 | AD-CAB_4013 | OA | 89 | synovium | 13S_S52_L001_R1_001.fastq.gz | pvt | 69 | F | No | Yes | Reverse | Left | 170.00 | 89.0 | 31.00 | 2 | Never_smoker | No | Yes | Yes | No | 2.9 | 81 | 85 | 5.1 | 5.4 | 5.9 | Yes | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
14.1_S54 | AD-CAB_3014 | RC | 66 | capsule | 14-1_S54_L001_R1_001.fastq.gz | NA | 70 | M | NA | NA | NA | Left | 1.77 | 100.0 | 32.00 | 3 | Ever_smoker | No | Yes | Yes | No | 2.9 | 86 | 79 | 7.1 | 6.3 | 5.8 | Yes | Intact | 50 | 45 | 95 | 27 | 43 | 47 | 47 | 50.0 | 9.1 | 6.8 | 9.1 | 12221 | 11111 | 11111 | 11111 | 90 | 90 | 88 | 85 |
14.2_S80 | AD-CAB_3014 | RC | 66 | tendon | 14-2_S80_L001_R1_001.fastq.gz | NA | 70 | M | NA | NA | NA | Left | 1.77 | 100.0 | 32.00 | 3 | Ever_smoker | No | Yes | Yes | No | 2.9 | 86 | 79 | 7.1 | 6.3 | 5.8 | Yes | Intact | 50 | 45 | 95 | 27 | 43 | 47 | 47 | 50.0 | 9.1 | 6.8 | 9.1 | 12221 | 11111 | 11111 | 11111 | 90 | 90 | 88 | 85 |
14.3_S106 | AD-CAB_3014 | RC | 66 | tear | 14-3_S106_L001_R1_001.fastq.gz | NA | 70 | M | NA | NA | NA | Left | 1.77 | 100.0 | 32.00 | 3 | Ever_smoker | No | Yes | Yes | No | 2.9 | 86 | 79 | 7.1 | 6.3 | 5.8 | Yes | Intact | 50 | 45 | 95 | 27 | 43 | 47 | 47 | 50.0 | 9.1 | 6.8 | 9.1 | 12221 | 11111 | 11111 | 11111 | 90 | 90 | 88 | 85 |
14B_S25 | AD-CAB_4014 | OA | 92 | bone | 14B_S25_L001_R1_001.fastq.gz | pvt | 71 | M | Yes | No | Reverse | Right | 170.00 | 99.0 | 34.00 | 2 | Ever_smoker | No | Yes | No | Yes | 2.9 | 69 | 90 | 7.0 | 7.0 | 7.1 | Yes | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
14C_S39 | AD-CAB_4014 | OA | 92 | capsule | 14C_S39_L001_R1_001.fastq.gz | pvt | 71 | M | No | Yes | Reverse | Right | 170.00 | 99.0 | 34.00 | 2 | Ever_smoker | No | Yes | No | Yes | 2.9 | 69 | 90 | 7.0 | 7.0 | 7.1 | Yes | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
14S_S53 | AD-CAB_4014 | OA | 92 | synovium | 14S_S53_L001_R1_001.fastq.gz | pvt | 71 | M | Yes | No | Reverse | Right | 170.00 | 99.0 | 34.00 | 2 | Ever_smoker | No | Yes | No | Yes | 2.9 | 69 | 90 | 7.0 | 7.0 | 7.1 | Yes | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
15.1_S55 | AD-CAB_3015 | RC | 69 | capsule | 15-1_S55_L001_R1_001.fastq.gz | NA | 66 | M | NA | NA | NA | Left | 175.00 | 95.0 | 31.00 | 3 | Never_smoker | No | Yes | Yes | No | 2.9 | 53 | 90 | 4.1 | 5.5 | 5.2 | Yes | Intact | 50 | 47 | 97 | 25 | NA | NA | 48 | 40.9 | NA | NA | 13.6 | 11121 | NA | NA | 11121 | 78 | NA | NA | 93 |
15.2_S81 | AD-CAB_3015 | RC | 69 | tendon | 15-2_S81_L001_R1_001.fastq.gz | NA | 66 | M | NA | NA | NA | Left | 175.00 | 95.0 | 31.00 | 3 | Never_smoker | No | Yes | Yes | No | 2.9 | 53 | 90 | 4.1 | 5.5 | 5.2 | Yes | Intact | 50 | 47 | 97 | 25 | NA | NA | 48 | 40.9 | NA | NA | 13.6 | 11121 | NA | NA | 11121 | 78 | NA | NA | 93 |
15.3_S107 | AD-CAB_3015 | RC | 69 | tear | 15-3_S107_L001_R1_001.fastq.gz | NA | 66 | M | NA | NA | NA | Left | 175.00 | 95.0 | 31.00 | 3 | Never_smoker | No | Yes | Yes | No | 2.9 | 53 | 90 | 4.1 | 5.5 | 5.2 | Yes | Intact | 50 | 47 | 97 | 25 | NA | NA | 48 | 40.9 | NA | NA | 13.6 | 11121 | NA | NA | 11121 | 78 | NA | NA | 93 |
15B_S26 | AD-CAB_4015 | OA | 93 | bone | 15B_S26_L001_R1_001.fastq.gz | pvt | 76 | M | Yes | No | Anatomic | Left | 183.00 | 95.0 | 28.00 | 2 | Ever_smoker | No | Yes | Yes | No | 5.6 | 90 | 71 | 6.6 | 5.5 | 5.0 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
15C_S40 | AD-CAB_4015 | OA | 93 | capsule | 15C_S40_L001_R1_001.fastq.gz | pvt | 76 | M | Yes | No | Anatomic | Left | 183.00 | 95.0 | 28.00 | 2 | Ever_smoker | No | Yes | Yes | No | 5.6 | 90 | 71 | 6.6 | 5.5 | 5.0 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
15S_S54 | AD-CAB_4015 | OA | 93 | synovium | 15S_S54_L001_R1_001.fastq.gz | pvt | 76 | M | Yes | No | Anatomic | Left | 183.00 | 95.0 | 28.00 | 2 | Ever_smoker | No | Yes | Yes | No | 5.6 | 90 | 71 | 6.6 | 5.5 | 5.0 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
16.1_S56 | AD-CAB_3016 | RC | 71 | capsule | 16-1_S56_L001_R1_001.fastq.gz | NA | 68 | M | NA | NA | NA | Left | 180.00 | 88.0 | 27.00 | 1 | Ever_smoker | Yes | No | Yes | No | 2.9 | 73 | 90 | 4.7 | 7.3 | 8.3 | No | Torn | 40 | 42 | 82 | 24 | 27 | 45 | 43 | 43.2 | 38.6 | 6.8 | 11.4 | 11122 | 11222 | 11112 | 11121 | 70 | 60 | 50 | 80 |
16.2_S82 | AD-CAB_3016 | RC | 71 | tendon | 16-2_S82_L001_R1_001.fastq.gz | NA | 68 | M | NA | NA | NA | Left | 180.00 | 88.0 | 27.00 | 1 | Ever_smoker | Yes | No | Yes | No | 2.9 | 73 | 90 | 4.7 | 7.3 | 8.3 | No | Torn | 40 | 42 | 82 | 24 | 27 | 45 | 43 | 43.2 | 38.6 | 6.8 | 11.4 | 11122 | 11222 | 11112 | 11121 | 70 | 60 | 50 | 80 |
16.3_S108 | AD-CAB_3016 | RC | 71 | tear | 16-3_S108_L001_R1_001.fastq.gz | NA | 68 | M | NA | NA | NA | Left | 180.00 | 88.0 | 27.00 | 1 | Ever_smoker | Yes | No | Yes | No | 2.9 | 73 | 90 | 4.7 | 7.3 | 8.3 | No | Torn | 40 | 42 | 82 | 24 | 27 | 45 | 43 | 43.2 | 38.6 | 6.8 | 11.4 | 11122 | 11222 | 11112 | 11121 | 70 | 60 | 50 | 80 |
16B_S27 | AD-CAB_4016 | OA | 99 | bone | 16B_S27_L001_R1_001.fastq.gz | pvt | 76 | F | Yes | No | Anatomic | Left | 167.00 | 54.0 | 19.00 | 3 | Ever_smoker | No | No | No | Yes | 2.9 | 60 | 86 | 11.0 | 4.7 | 5.3 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
16C_S41 | AD-CAB_4016 | OA | 99 | capsule | 16C_S41_L001_R1_001.fastq.gz | pvt | 76 | F | Yes | No | Anatomic | Left | 167.00 | 54.0 | 19.00 | 3 | Ever_smoker | No | No | No | Yes | 2.9 | 60 | 86 | 11.0 | 4.7 | 5.3 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
16S_S55 | AD-CAB_4016 | OA | 99 | synovium | 16S_S55_L001_R1_001.fastq.gz | pvt | 76 | F | Yes | No | Anatomic | Left | 167.00 | 54.0 | 19.00 | 3 | Ever_smoker | No | No | No | Yes | 2.9 | 60 | 86 | 11.0 | 4.7 | 5.3 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
17.1_S57 | AD-CAB_3017 | RC | 70 | capsule | 17-1_S57_L001_R1_001.fastq.gz | NA | 60 | M | NA | NA | NA | Left | 166.00 | 80.0 | 29.00 | 2 | Ever_smoker | No | No | No | No | 2.9 | 119 | 57 | 7.2 | NA | 5.7 | No | Torn | NA | NA | NA | 13 | 40 | NA | NA | 93.2 | 38.6 | NA | NA | 12221 | 21211 | NA | NA | 70 | 60 | NA | NA |
17.2_S83 | AD-CAB_3017 | RC | 70 | tendon | 17-2_S83_L001_R1_001.fastq.gz | NA | 60 | M | NA | NA | NA | Left | 166.00 | 80.0 | 29.00 | 2 | Ever_smoker | No | No | No | No | 2.9 | 119 | 57 | 7.2 | NA | 5.7 | No | Torn | NA | NA | NA | 13 | 40 | NA | NA | 93.2 | 38.6 | NA | NA | 12221 | 21211 | NA | NA | 70 | 60 | NA | NA |
17.3_S109 | AD-CAB_3017 | RC | 70 | tear | 17-3_S109_L001_R1_001.fastq.gz | NA | 60 | M | NA | NA | NA | Left | 166.00 | 80.0 | 29.00 | 2 | Ever_smoker | No | No | No | No | 2.9 | 119 | 57 | 7.2 | NA | 5.7 | No | Torn | NA | NA | NA | 13 | 40 | NA | NA | 93.2 | 38.6 | NA | NA | 12221 | 21211 | NA | NA | 70 | 60 | NA | NA |
17B_S28 | AD-CAB_4017 | OA | 96 | bone | 17B_S28_L001_R1_001.fastq.gz | pvt | 79 | F | Yes | No | Reverse | Right | 155.00 | 75.0 | 31.00 | 2 | Never_smoker | No | No | No | No | 9.2 | 71 | 70 | 4.5 | 5.5 | 5.1 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
17C_S42 | AD-CAB_4017 | OA | 96 | capsule | 17C_S42_L001_R1_001.fastq.gz | pvt | 79 | F | No | Yes | Reverse | Right | 155.00 | 75.0 | 31.00 | 2 | Never_smoker | No | No | No | No | 9.2 | 71 | 70 | 4.5 | 5.5 | 5.1 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
17S_S56 | AD-CAB_4017 | OA | 96 | synovium | 17S_S56_L001_R1_001.fastq.gz | pvt | 79 | F | Yes | No | Reverse | Right | 155.00 | 75.0 | 31.00 | 2 | Never_smoker | No | No | No | No | 9.2 | 71 | 70 | 4.5 | 5.5 | 5.1 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
18.1_S58 | AD-CAB_3018 | RC | 72 | capsule | 18-1_S58_L001_R1_001.fastq.gz | NA | 72 | M | NA | NA | NA | Right | 170.00 | 85.0 | 29.00 | 2 | Ever_smoker | No | Yes | Yes | No | 3.2 | 82 | 82 | 6.4 | 5.5 | 5.5 | No | Intact | 50 | 50 | 100 | 36 | 37 | 48 | 48 | 31.8 | 13.6 | 9.1 | 0.0 | 11122 | 11112 | 11111 | 11111 | 90 | 82 | 92 | 90 |
18.2_S84 | AD-CAB_3018 | RC | 72 | tendon | 18-2_S84_L001_R1_001.fastq.gz | NA | 72 | M | NA | NA | NA | Right | 170.00 | 85.0 | 29.00 | 2 | Ever_smoker | No | Yes | Yes | No | 3.2 | 82 | 82 | 6.4 | 5.5 | 5.5 | No | Intact | 50 | 50 | 100 | 36 | 37 | 48 | 48 | 31.8 | 13.6 | 9.1 | 0.0 | 11122 | 11112 | 11111 | 11111 | 90 | 82 | 92 | 90 |
18.3_S110 | AD-CAB_3018 | RC | 72 | tear | 18-3_S110_L001_R1_001.fastq.gz | NA | 72 | M | NA | NA | NA | Right | 170.00 | 85.0 | 29.00 | 2 | Ever_smoker | No | Yes | Yes | No | 3.2 | 82 | 82 | 6.4 | 5.5 | 5.5 | No | Intact | 50 | 50 | 100 | 36 | 37 | 48 | 48 | 31.8 | 13.6 | 9.1 | 0.0 | 11122 | 11112 | 11111 | 11111 | 90 | 82 | 92 | 90 |
18B_S29 | AD-CAB_4018 | OA | 97 | bone | 18B_S29_L001_R1_001.fastq.gz | pvt | 73 | F | Yes | No | Anatomic | Right | 167.00 | 85.0 | 30.00 | 3 | Ever_smoker | No | Yes | No | No | 1.5 | 78 | 65 | 7.3 | 5.4 | 5.9 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
18C_S43 | AD-CAB_4018 | OA | 97 | capsule | 18C_S43_L001_R1_001.fastq.gz | pvt | 73 | F | Yes | No | Anatomic | Right | 167.00 | 85.0 | 30.00 | 3 | Ever_smoker | No | Yes | No | No | 1.5 | 78 | 65 | 7.3 | 5.4 | 5.9 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
18S_S57 | AD-CAB_4018 | OA | 97 | synovium | 18S_S57_L001_R1_001.fastq.gz | pvt | 73 | F | Yes | No | Anatomic | Right | 167.00 | 85.0 | 30.00 | 3 | Ever_smoker | No | Yes | No | No | 1.5 | 78 | 65 | 7.3 | 5.4 | 5.9 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
19.1_S59 | AD-CAB_3019 | RC | 73 | capsule | 19-1_S59_L001_R1_001.fastq.gz | NA | 45 | F | NA | NA | NA | Right | 163.00 | 98.0 | 36.90 | 2 | Never_smoker | No | Yes | Yes | No | 4.3 | 70 | 57 | 4.6 | 4.7 | 5.7 | Yes | Intact | 50 | 35 | 85 | 32 | 28 | 45 | 47 | 36.4 | 38.6 | 18.2 | 13.6 | 11221 | 11221 | 11121 | 11121 | 50 | 58 | 45 | 34 |
19.2_S85 | AD-CAB_3019 | RC | 73 | tendon | 19-2_S85_L001_R1_001.fastq.gz | NA | 45 | F | NA | NA | NA | Right | 163.00 | 98.0 | 36.90 | 2 | Never_smoker | No | Yes | Yes | No | 4.3 | 70 | 57 | 4.6 | 4.7 | 5.7 | Yes | Intact | 50 | 35 | 85 | 32 | 28 | 45 | 47 | 36.4 | 38.6 | 18.2 | 13.6 | 11221 | 11221 | 11121 | 11121 | 50 | 58 | 45 | 34 |
19.3_S111 | AD-CAB_3019 | RC | 73 | tear | 19-3_S111_L001_R1_001.fastq.gz | NA | 45 | F | NA | NA | NA | Right | 163.00 | 98.0 | 36.90 | 2 | Never_smoker | No | Yes | Yes | No | 4.3 | 70 | 57 | 4.6 | 4.7 | 5.7 | Yes | Intact | 50 | 35 | 85 | 32 | 28 | 45 | 47 | 36.4 | 38.6 | 18.2 | 13.6 | 11221 | 11221 | 11121 | 11121 | 50 | 58 | 45 | 34 |
19B_S30 | AD-CAB_4019 | OA | 95 | bone | 19B_S30_L001_R1_001.fastq.gz | pvt | 65 | F | Yes | No | Anatomic | Left | 170.00 | 62.0 | 21.00 | 2 | Never_smoker | No | No | Yes | No | 2.9 | 103 | 49 | 11.0 | 5.3 | 5.2 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
19C_S44 | AD-CAB_4019 | OA | 95 | capsule | 19C_S44_L001_R1_001.fastq.gz | pvt | 65 | F | Yes | No | Anatomic | Left | 170.00 | 62.0 | 21.00 | 2 | Never_smoker | No | No | Yes | No | 2.9 | 103 | 49 | 11.0 | 5.3 | 5.2 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
19S_S58 | AD-CAB_4019 | OA | 95 | synovium | 19S_S58_L001_R1_001.fastq.gz | pvt | 65 | F | Yes | No | Anatomic | Left | 170.00 | 62.0 | 21.00 | 2 | Never_smoker | No | No | Yes | No | 2.9 | 103 | 49 | 11.0 | 5.3 | 5.2 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
2.1_S42 | AD-CAB_3002 | RC | 54 | capsule | 2-1_S42_L001_R1_001.fastq.gz | NA | 58 | M | NA | NA | NA | Right | 179.00 | 79.0 | 25.00 | 1 | Never_smoker | No | No | No | No | 0.7 | 70 | 90 | 6.9 | 5.4 | 5.3 | No | Torn | NA | NA | NA | 33 | NA | 48 | NA | 29.5 | NA | 0.0 | NA | 11111 | NA | 11111 | NA | 90 | NA | 90 | NA |
2.2_S68 | AD-CAB_3002 | RC | 54 | tendon | 2-2_S68_L001_R1_001.fastq.gz | NA | 58 | M | NA | NA | NA | Right | 179.00 | 79.0 | 25.00 | 1 | Never_smoker | No | No | No | No | 0.7 | 70 | 90 | 6.9 | 5.4 | 5.3 | No | Torn | NA | NA | NA | 33 | NA | 48 | NA | 29.5 | NA | 0.0 | NA | 11111 | NA | 11111 | NA | 90 | NA | 90 | NA |
2.3_S94 | AD-CAB_3002 | RC | 54 | tear | 2-3_S94_L001_R1_001.fastq.gz | NA | 58 | M | NA | NA | NA | Right | 179.00 | 79.0 | 25.00 | 1 | Never_smoker | No | No | No | No | 0.7 | 70 | 90 | 6.9 | 5.4 | 5.3 | No | Torn | NA | NA | NA | 33 | NA | 48 | NA | 29.5 | NA | 0.0 | NA | 11111 | NA | 11111 | NA | 90 | NA | 90 | NA |
20.1_S60 | AD-CAB_3020 | RC | 67 | capsule | 20-1_S60_L001_R1_001.fastq.gz | NA | 61 | M | NA | NA | NA | Right | 180.00 | 92.0 | 29.00 | 1 | Ever_smoker | No | No | No | No | 2.9 | 78 | 57 | 3.9 | 5.5 | 5.6 | No | Intact | 50 | 40 | 90 | 30 | 34 | 36 | 44 | 50.0 | 34.1 | 31.8 | 0.0 | 12321 | 12321 | 12211 | 12211 | 77 | 40 | 70 | 70 |
20.2_S86 | AD-CAB_3020 | RC | 67 | tendon | 20-2_S86_L001_R1_001.fastq.gz | NA | 61 | M | NA | NA | NA | Right | 180.00 | 92.0 | 29.00 | 1 | Ever_smoker | No | No | No | No | 2.9 | 78 | 57 | 3.9 | 5.5 | 5.6 | No | Intact | 50 | 40 | 90 | 30 | 34 | 36 | 44 | 50.0 | 34.1 | 31.8 | 0.0 | 12321 | 12321 | 12211 | 12211 | 77 | 40 | 70 | 70 |
20.3_S112 | AD-CAB_3020 | RC | 67 | tear | 20-3_S112_L001_R1_001.fastq.gz | NA | 61 | M | NA | NA | NA | Right | 180.00 | 92.0 | 29.00 | 1 | Ever_smoker | No | No | No | No | 2.9 | 78 | 57 | 3.9 | 5.5 | 5.6 | No | Intact | 50 | 40 | 90 | 30 | 34 | 36 | 44 | 50.0 | 34.1 | 31.8 | 0.0 | 12321 | 12321 | 12211 | 12211 | 77 | 40 | 70 | 70 |
20B_S31 | AD-CAB_4020 | OA | 98 | bone | 20B_S31_L001_R1_001.fastq.gz | pvt | 62 | M | Yes | No | Anatomic | Left | 180.00 | 117.0 | 36.00 | 2 | Never_smoker | No | Yes | No | No | 2.9 | 80 | 90 | 4.9 | 6.9 | 5.9 | Yes | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
20C_S45 | AD-CAB_4020 | OA | 98 | capsule | 20C_S45_L001_R1_001.fastq.gz | pvt | 62 | M | Yes | No | Anatomic | Left | 180.00 | 117.0 | 36.00 | 2 | Never_smoker | No | Yes | No | No | 2.9 | 80 | 90 | 4.9 | 6.9 | 5.9 | Yes | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
20S_S59 | AD-CAB_4020 | OA | 98 | synovium | 20S_S59_L001_R1_001.fastq.gz | pvt | 62 | M | Yes | No | Anatomic | Left | 180.00 | 117.0 | 36.00 | 2 | Never_smoker | No | Yes | No | No | 2.9 | 80 | 90 | 4.9 | 6.9 | 5.9 | Yes | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
21.1_S61 | AD-CAB_3021 | RC | 68 | capsule | 21-1_S61_L001_R1_001.fastq.gz | NA | 46 | M | NA | NA | NA | Right | 180.00 | 88.0 | 27.20 | 2 | Never_smoker | No | Yes | No | No | 2.9 | 77 | 57 | 5.9 | 5.9 | 5.3 | No | Torn | NA | NA | NA | 29 | 44 | 43 | NA | 45.5 | 20.5 | 11.4 | NA | NA | 11111 | 11121 | NA | NA | 80 | 65 | NA |
21.2_S87 | AD-CAB_3021 | RC | 68 | tendon | 21-2_S87_L001_R1_001.fastq.gz | NA | 46 | M | NA | NA | NA | Right | 180.00 | 88.0 | 27.20 | 2 | Never_smoker | No | Yes | No | No | 2.9 | 77 | 57 | 5.9 | 5.9 | 5.3 | No | Torn | NA | NA | NA | 29 | 44 | 43 | NA | 45.5 | 20.5 | 11.4 | NA | NA | 11111 | 11121 | NA | NA | 80 | 65 | NA |
21.3_S113 | AD-CAB_3021 | RC | 68 | tear | 21-3_S113_L001_R1_001.fastq.gz | NA | 46 | M | NA | NA | NA | Right | 180.00 | 88.0 | 27.20 | 2 | Never_smoker | No | Yes | No | No | 2.9 | 77 | 57 | 5.9 | 5.9 | 5.3 | No | Torn | NA | NA | NA | 29 | 44 | 43 | NA | 45.5 | 20.5 | 11.4 | NA | NA | 11111 | 11121 | NA | NA | 80 | 65 | NA |
22.1_S62 | AD-CAB_3022 | RC | 74 | capsule | 22-1_S62_L001_R1_001.fastq.gz | NA | 39 | F | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | 25 | NA | NA | NA | 47.7 | NA | NA | NA | 12222 | NA | NA | NA | 30 | NA | NA | NA |
22.2_S88 | AD-CAB_3022 | RC | 74 | tendon | 22-2_S88_L001_R1_001.fastq.gz | NA | 39 | F | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | 25 | NA | NA | NA | 47.7 | NA | NA | NA | 12222 | NA | NA | NA | 30 | NA | NA | NA |
22.3_S114 | AD-CAB_3022 | RC | 74 | tear | 22-3_S114_L001_R1_001.fastq.gz | NA | 39 | F | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | 25 | NA | NA | NA | 47.7 | NA | NA | NA | 12222 | NA | NA | NA | 30 | NA | NA | NA |
23.1_S63 | AD-CAB_3023 | RC | 75 | capsule | 23-1_S63_L001_R1_001.fastq.gz | NA | 58 | M | NA | NA | NA | Right | 179.00 | 81.0 | 25.00 | 2 | Ever_smoker | No | Yes | No | No | 2.9 | 75 | 57 | 5.7 | 5.4 | 5.7 | No | Intact | 50 | 40 | 90 | 42 | 43 | 48 | 48 | 15.9 | 15.9 | 0.0 | 2.3 | 11211 | 11121 | 11111 | 11111 | 85 | 85 | 90 | 85 |
23.2_S89 | AD-CAB_3023 | RC | 75 | tendon | 23-2_S89_L001_R1_001.fastq.gz | NA | 58 | M | NA | NA | NA | Right | 179.00 | 81.0 | 25.00 | 2 | Ever_smoker | No | Yes | No | No | 2.9 | 75 | 57 | 5.7 | 5.4 | 5.7 | No | Intact | 50 | 40 | 90 | 42 | 43 | 48 | 48 | 15.9 | 15.9 | 0.0 | 2.3 | 11211 | 11121 | 11111 | 11111 | 85 | 85 | 90 | 85 |
23.3_S115 | AD-CAB_3023 | RC | 75 | tear | 23-3_S115_L001_R1_001.fastq.gz | NA | 58 | M | NA | NA | NA | Right | 179.00 | 81.0 | 25.00 | 2 | Ever_smoker | No | Yes | No | No | 2.9 | 75 | 57 | 5.7 | 5.4 | 5.7 | No | Intact | 50 | 40 | 90 | 42 | 43 | 48 | 48 | 15.9 | 15.9 | 0.0 | 2.3 | 11211 | 11121 | 11111 | 11111 | 85 | 85 | 90 | 85 |
24.1_S64 | AD-CAB_3024 | RC | 76 | capsule | 24-1_S64_L001_R1_001.fastq.gz | NA | 52 | F | NA | NA | NA | Right | 153.00 | 70.0 | 28.00 | 2 | Never_smoker | No | Yes | Yes | Yes | 3.0 | 64 | 57 | 7.8 | 5.6 | 6.4 | No | NA | NA | NA | NA | 26 | 23 | NA | NA | 56.8 | 45.5 | NA | NA | 12222 | 12221 | NA | NA | 30 | 60 | NA | NA |
24.2_S90 | AD-CAB_3024 | RC | 76 | tendon | 24-2_S90_L001_R1_001.fastq.gz | NA | 52 | F | NA | NA | NA | Right | 153.00 | 70.0 | 28.00 | 2 | Never_smoker | No | Yes | Yes | Yes | 3.0 | 64 | 57 | 7.8 | 5.6 | 6.4 | No | NA | NA | NA | NA | 26 | 23 | NA | NA | 56.8 | 45.5 | NA | NA | 12222 | 12221 | NA | NA | 30 | 60 | NA | NA |
24.3_S116 | AD-CAB_3024 | RC | 76 | tear | 24-3_S116_L001_R1_001.fastq.gz | NA | 52 | F | NA | NA | NA | Right | 153.00 | 70.0 | 28.00 | 2 | Never_smoker | No | Yes | Yes | Yes | 3.0 | 64 | 57 | 7.8 | 5.6 | 6.4 | No | NA | NA | NA | NA | 26 | 23 | NA | NA | 56.8 | 45.5 | NA | NA | 12222 | 12221 | NA | NA | 30 | 60 | NA | NA |
25.1_S65 | AD-CAB_3025 | RC | 77 | capsule | 25-1_S65_L001_R1_001.fastq.gz | NA | 62 | F | NA | NA | NA | Left | 157.00 | 95.0 | 38.50 | 2 | Never_smoker | No | Yes | Yes | No | 12.0 | 72 | 57 | 6.6 | 6.2 | 5.7 | Yes | Intact | 45 | 43 | 88 | 26 | 36 | 38 | 41 | 59.1 | 29.5 | 31.8 | 18.2 | 12231 | 11221 | 11221 | 11121 | 82 | 80 | 60 | 80 |
25.2_S91 | AD-CAB_3025 | RC | 77 | tendon | 25-2_S91_L001_R1_001.fastq.gz | NA | 62 | F | NA | NA | NA | Left | 157.00 | 95.0 | 38.50 | 2 | Never_smoker | No | Yes | Yes | No | 12.0 | 72 | 57 | 6.6 | 6.2 | 5.7 | Yes | Intact | 45 | 43 | 88 | 26 | 36 | 38 | 41 | 59.1 | 29.5 | 31.8 | 18.2 | 12231 | 11221 | 11221 | 11121 | 82 | 80 | 60 | 80 |
25.3_S117 | AD-CAB_3025 | RC | 77 | tear | 25-3_S117_L001_R1_001.fastq.gz | NA | 62 | F | NA | NA | NA | Left | 157.00 | 95.0 | 38.50 | 2 | Never_smoker | No | Yes | Yes | No | 12.0 | 72 | 57 | 6.6 | 6.2 | 5.7 | Yes | Intact | 45 | 43 | 88 | 26 | 36 | 38 | 41 | 59.1 | 29.5 | 31.8 | 18.2 | 12231 | 11221 | 11221 | 11121 | 82 | 80 | 60 | 80 |
26.1_S66 | AD-CAB_3026 | RC | 79 | capsule | 26-1_S66_L001_R1_001.fastq.gz | NA | 59 | M | NA | NA | NA | Right | 176.00 | 104.0 | 33.70 | 2 | Ever_smoker | No | Yes | Yes | No | 2.9 | 62 | 57 | 4.2 | 3.6 | 5.3 | Yes | NA | NA | NA | NA | 30 | 42 | 44 | NA | 38.6 | 25.0 | 22.7 | NA | 12222 | 11222 | 11221 | NA | 70 | 90 | 90 | NA |
26.2_S92 | AD-CAB_3026 | RC | 79 | tendon | 26-2_S92_L001_R1_001.fastq.gz | NA | 59 | M | NA | NA | NA | Right | 176.00 | 104.0 | 33.70 | 2 | Ever_smoker | No | Yes | Yes | No | 2.9 | 62 | 57 | 4.2 | 3.6 | 5.3 | Yes | NA | NA | NA | NA | 30 | 42 | 44 | NA | 38.6 | 25.0 | 22.7 | NA | 12222 | 11222 | 11221 | NA | 70 | 90 | 90 | NA |
26.3_S118 | AD-CAB_3026 | RC | 79 | tear | 26-3_S118_L001_R1_001.fastq.gz | NA | 59 | M | NA | NA | NA | Right | 176.00 | 104.0 | 33.70 | 2 | Ever_smoker | No | Yes | Yes | No | 2.9 | 62 | 57 | 4.2 | 3.6 | 5.3 | Yes | NA | NA | NA | NA | 30 | 42 | 44 | NA | 38.6 | 25.0 | 22.7 | NA | 12222 | 11222 | 11221 | NA | 70 | 90 | 90 | NA |
3.1_S43 | AD-CAB_3003 | RC | 55 | capsule | 3-1_S43_L001_R1_001.fastq.gz | NA | 56 | M | NA | NA | NA | Left | 179.00 | 85.0 | 26.52 | 1 | Never_smoker | No | Yes | NA | No | 2.9 | 72 | 90 | 4.3 | 5.2 | 5.4 | No | Intact | 50 | 50 | 100 | 38 | 38 | 44 | 48 | 29.5 | 27.3 | 9.1 | 0.0 | 11221 | 11121 | 11111 | 22222 | 80 | 70 | 80 | 60 |
3.2_S69 | AD-CAB_3003 | RC | 55 | tendon | 3-2_S69_L001_R1_001.fastq.gz | NA | 56 | M | NA | NA | NA | Left | 179.00 | 85.0 | 26.52 | 1 | Never_smoker | No | Yes | NA | No | 2.9 | 72 | 90 | 4.3 | 5.2 | 5.4 | No | Intact | 50 | 50 | 100 | 38 | 38 | 44 | 48 | 29.5 | 27.3 | 9.1 | 0.0 | 11221 | 11121 | 11111 | 22222 | 80 | 70 | 80 | 60 |
3.3_S95 | AD-CAB_3003 | RC | 55 | tear | 3-3_S95_L001_R1_001.fastq.gz | NA | 56 | M | NA | NA | NA | Left | 179.00 | 85.0 | 26.52 | 1 | Never_smoker | No | Yes | NA | No | 2.9 | 72 | 90 | 4.3 | 5.2 | 5.4 | No | Intact | 50 | 50 | 100 | 38 | 38 | 44 | 48 | 29.5 | 27.3 | 9.1 | 0.0 | 11221 | 11121 | 11111 | 22222 | 80 | 70 | 80 | 60 |
4.1_S44 | AD-CAB_3004 | RC | 56 | capsule | 4-1_S44_L001_R1_001.fastq.gz | NA | 68 | M | NA | NA | NA | Right | 185.00 | 95.0 | 28.00 | 2 | Ever_smoker | No | Yes | Yes | No | 3.6 | 91 | 74 | 7.8 | 6.7 | 5.7 | No | Intact | 45 | 50 | 95 | 24 | 41 | 46 | 48 | NA | 18.2 | 13.6 | 0.0 | 11232 | 11121 | 11121 | 11111 | NA | 80 | 60 | 52 |
4.2_S70 | AD-CAB_3004 | RC | 56 | tendon | 4-2_S70_L001_R1_001.fastq.gz | NA | 68 | M | NA | NA | NA | Right | 185.00 | 95.0 | 28.00 | 2 | Ever_smoker | No | Yes | Yes | No | 3.6 | 91 | 74 | 7.8 | 6.7 | 5.7 | No | Intact | 45 | 50 | 95 | 24 | 41 | 46 | 48 | NA | 18.2 | 13.6 | 0.0 | 11232 | 11121 | 11121 | 11111 | NA | 80 | 60 | 52 |
4.3_S96 | AD-CAB_3004 | RC | 56 | tear | 4-3_S96_L001_R1_001.fastq.gz | NA | 68 | M | NA | NA | NA | Right | 185.00 | 95.0 | 28.00 | 2 | Ever_smoker | No | Yes | Yes | No | 3.6 | 91 | 74 | 7.8 | 6.7 | 5.7 | No | Intact | 45 | 50 | 95 | 24 | 41 | 46 | 48 | NA | 18.2 | 13.6 | 0.0 | 11232 | 11121 | 11121 | 11111 | NA | 80 | 60 | 52 |
4001.41B | AD-CAB_4001 | OA | 84 | bone | 4001-41B_R1_001.fastq.gz | pvt | 69 | F | Yes | No | Anatomic | Left | 158.00 | 89.0 | 36.00 | 2 | Never_smoker | No | Yes | Yes | Yes | 2.9 | 66 | 82 | 5.2 | 5.7 | 6.1 | Yes | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
4001.41C | AD-CAB_4001 | OA | 84 | capsule | 4001-41C_R1_001.fastq.gz | pvt | 69 | F | Yes | No | Anatomic | Left | 158.00 | 89.0 | 36.00 | 2 | Never_smoker | No | Yes | Yes | Yes | 2.9 | 66 | 82 | 5.2 | 5.7 | 6.1 | Yes | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
4001.41S | AD-CAB_4001 | OA | 84 | synovium | 4001-41S_R1_001.fastq.gz | pvt | 69 | F | Yes | No | Anatomic | Left | 158.00 | 89.0 | 36.00 | 2 | Never_smoker | No | Yes | Yes | Yes | 2.9 | 66 | 82 | 5.2 | 5.7 | 6.1 | Yes | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
4002.42B | AD-CAB_4002 | OA | 80 | bone | 4002-42B_R1_001.fastq.gz | pvt | 59 | M | Yes | No | Anatomic | Left | 182.00 | 106.0 | 32.00 | 1 | Ever_smoker | No | Yes | No | No | 9.3 | 69 | 90 | 4.3 | 6.2 | 5.4 | Yes | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
4002.42C | AD-CAB_4002 | OA | 80 | capsule | 4002-42C_R1_001.fastq.gz | pvt | 59 | M | Yes | No | Anatomic | Left | 182.00 | 106.0 | 32.00 | 1 | Ever_smoker | No | Yes | No | No | 9.3 | 69 | 90 | 4.3 | 6.2 | 5.4 | Yes | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
4002.42S | AD-CAB_4002 | OA | 80 | synovium | 4002-42S_R1_001.fastq.gz | pvt | 59 | M | Yes | No | Anatomic | Left | 182.00 | 106.0 | 32.00 | 1 | Ever_smoker | No | Yes | No | No | 9.3 | 69 | 90 | 4.3 | 6.2 | 5.4 | Yes | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
4003.43B | AD-CAB_4003 | OA | 81 | bone | 4003-43B_R1_001.fastq.gz | pvt | 74 | F | No | Yes | Reverse | Right | 153.00 | 87.0 | 37.00 | 2 | Ever_smoker | No | Yes | Yes | No | 6.9 | 77 | 66 | 5.0 | 5.4 | 5.4 | Yes | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
4003.43C | AD-CAB_4003 | OA | 81 | capsule | 4003-43C_R1_001.fastq.gz | pvt | 74 | F | No | Yes | Reverse | Right | 153.00 | 87.0 | 37.00 | 2 | Ever_smoker | No | Yes | Yes | No | 6.9 | 77 | 66 | 5.0 | 5.4 | 5.4 | Yes | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
4003.43S | AD-CAB_4003 | OA | 81 | synovium | 4003-43S_R1_001.fastq.gz | pvt | 74 | F | No | Yes | Reverse | Right | 153.00 | 87.0 | 37.00 | 2 | Ever_smoker | No | Yes | Yes | No | 6.9 | 77 | 66 | 5.0 | 5.4 | 5.4 | Yes | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
4004.44B | AD-CAB_4004 | OA | 82 | bone | 4004-44B_R1_001.fastq.gz | pvt | 69 | F | Yes | No | Anatomic | Left | 165.00 | 85.0 | 32.00 | 2 | Never_smoker | No | Yes | Yes | Yes | 3.9 | 61 | 89 | 5.8 | 5.8 | 5.6 | Yes | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
4004.44C | AD-CAB_4004 | OA | 82 | capsule | 4004-44C_R1_001.fastq.gz | pvt | 69 | F | Yes | No | Anatomic | Left | 165.00 | 85.0 | 32.00 | 2 | Never_smoker | No | Yes | Yes | Yes | 3.9 | 61 | 89 | 5.8 | 5.8 | 5.6 | Yes | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
4004.44S | AD-CAB_4004 | OA | 82 | synovium | 4004-44S_R1_001.fastq.gz | pvt | 69 | F | Yes | No | Anatomic | Left | 165.00 | 85.0 | 32.00 | 2 | Never_smoker | No | Yes | Yes | Yes | 3.9 | 61 | 89 | 5.8 | 5.8 | 5.6 | Yes | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
4005.45B | AD-CAB_4005 | OA | 83 | bone | 4005-45B_R1_001.fastq.gz | pvt | 74 | F | Yes | No | Anatomic | Left | 169.00 | 75.0 | 26.00 | 2 | Ever_smoker | No | Yes | Yes | No | 2.9 | 90 | 72 | 6.6 | 5.2 | 5.7 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
4005.45C | AD-CAB_4005 | OA | 83 | capsule | 4005-45C_R1_001.fastq.gz | pvt | 74 | F | Yes | No | Anatomic | Left | 169.00 | 75.0 | 26.00 | 2 | Ever_smoker | No | Yes | Yes | No | 2.9 | 90 | 72 | 6.6 | 5.2 | 5.7 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
4005.45S | AD-CAB_4005 | OA | 83 | synovium | 4005-45S_R1_001.fastq.gz | pvt | 74 | F | Yes | No | Anatomic | Left | 169.00 | 75.0 | 26.00 | 2 | Ever_smoker | No | Yes | Yes | No | 2.9 | 90 | 72 | 6.6 | 5.2 | 5.7 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
4006.46B | AD-CAB_4006 | OA | 78 | bone | 4006-46B_R1_001.fastq.gz | pvt | 81 | F | Yes | No | Anatomic | Right | 150.00 | 54.0 | 24.00 | 3 | Never_smoker | No | Yes | Yes | No | 2.9 | 105 | 43 | 10.5 | 5.6 | 6.0 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
4006.46C | AD-CAB_4006 | OA | 78 | capsule | 4006-46C_R1_001.fastq.gz | pvt | 81 | F | Yes | No | Anatomic | Right | 150.00 | 54.0 | 24.00 | 3 | Never_smoker | No | Yes | Yes | No | 2.9 | 105 | 43 | 10.5 | 5.6 | 6.0 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
4006.46S | AD-CAB_4006 | OA | 78 | synovium | 4006-46S_R1_001.fastq.gz | pvt | 81 | F | Yes | No | Anatomic | Right | 150.00 | 54.0 | 24.00 | 3 | Never_smoker | No | Yes | Yes | No | 2.9 | 105 | 43 | 10.5 | 5.6 | 6.0 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
5.1_S45 | AD-CAB_3005 | RC | 57 | capsule | 5-1_S45_L001_R1_001.fastq.gz | NA | 59 | F | NA | NA | NA | Right | NA | NA | NA | 1 | Never_smoker | No | No | No | No | 3.8 | 51 | 90 | 6.2 | NA | 5.2 | NA | Torn | 50 | 50 | 100 | 38 | 45 | NA | 48 | 25.0 | 4.5 | NA | 0.0 | 11121 | 11111 | NA | 11111 | 92 | 94 | 95 | NA |
5.2_S71 | AD-CAB_3005 | RC | 57 | tendon | 5-2_S71_L001_R1_001.fastq.gz | NA | 59 | F | NA | NA | NA | Right | NA | NA | NA | 1 | Never_smoker | No | No | No | No | 3.8 | 51 | 90 | 6.2 | NA | 5.2 | NA | Torn | 50 | 50 | 100 | 38 | 45 | NA | 48 | 25.0 | 4.5 | NA | 0.0 | 11121 | 11111 | NA | 11111 | 92 | 94 | 95 | NA |
5.3_S97 | AD-CAB_3005 | RC | 57 | tear | 5-3_S97_L001_R1_001.fastq.gz | NA | 59 | F | NA | NA | NA | Right | NA | NA | NA | 1 | Never_smoker | No | No | No | No | 3.8 | 51 | 90 | 6.2 | NA | 5.2 | NA | Torn | 50 | 50 | 100 | 38 | 45 | NA | 48 | 25.0 | 4.5 | NA | 0.0 | 11121 | 11111 | NA | 11111 | 92 | 94 | 95 | NA |
6.1_S46 | AD-CAB_3006 | RC | 58 | capsule | 6-1_S46_L001_R1_001.fastq.gz | NA | 65 | M | NA | NA | NA | Left | 172.00 | 78.0 | 26.00 | 1 | Never_smoker | No | No | No | No | 2.9 | 77 | 90 | 5.6 | 4.8 | 5.4 | No | Torn | NA | NA | NA | 35 | 31 | 37 | NA | 34.1 | 36.4 | 27.3 | NA | 12221 | 11221 | 11111 | NA | 82 | 40 | 80 | NA |
6.2_S72 | AD-CAB_3006 | RC | 58 | tendon | 6-2_S72_L001_R1_001.fastq.gz | NA | 65 | M | NA | NA | NA | Left | 172.00 | 78.0 | 26.00 | 1 | Never_smoker | No | No | No | No | 2.9 | 77 | 90 | 5.6 | 4.8 | 5.4 | No | Torn | NA | NA | NA | 35 | 31 | 37 | NA | 34.1 | 36.4 | 27.3 | NA | 12221 | 11221 | 11111 | NA | 82 | 40 | 80 | NA |
6.3_S98 | AD-CAB_3006 | RC | 58 | tear | 6-3_S98_L001_R1_001.fastq.gz | NA | 65 | M | NA | NA | NA | Left | 172.00 | 78.0 | 26.00 | 1 | Never_smoker | No | No | No | No | 2.9 | 77 | 90 | 5.6 | 4.8 | 5.4 | No | Torn | NA | NA | NA | 35 | 31 | 37 | NA | 34.1 | 36.4 | 27.3 | NA | 12221 | 11221 | 11111 | NA | 82 | 40 | 80 | NA |
7.1_S47 | AD-CAB_3007 | RC | 59 | capsule | 7-1_S47_L001_R1_001.fastq.gz | NA | 63 | F | NA | NA | NA | Right | 163.00 | 57.0 | 21.50 | 1 | Ever_smoker | No | No | No | No | 2.9 | 53 | 90 | 29.0 | NA | 5.3 | No | Intact | 50 | 50 | 100 | 37 | 38 | 46 | 48 | 36.4 | 18.2 | 11.4 | 2.3 | 11122 | 11111 | 11111 | 11111 | 93 | 97 | 100 | 100 |
7.2_S73 | AD-CAB_3007 | RC | 59 | tendon | 7-2_S73_L001_R1_001.fastq.gz | NA | 63 | F | NA | NA | NA | Right | 163.00 | 57.0 | 21.50 | 1 | Ever_smoker | No | No | No | No | 2.9 | 53 | 90 | 29.0 | NA | 5.3 | No | Intact | 50 | 50 | 100 | 37 | 38 | 46 | 48 | 36.4 | 18.2 | 11.4 | 2.3 | 11122 | 11111 | 11111 | 11111 | 93 | 97 | 100 | 100 |
7.3_S99 | AD-CAB_3007 | RC | 59 | tear | 7-3_S99_L001_R1_001.fastq.gz | NA | 63 | F | NA | NA | NA | Right | 163.00 | 57.0 | 21.50 | 1 | Ever_smoker | No | No | No | No | 2.9 | 53 | 90 | 29.0 | NA | 5.3 | No | Intact | 50 | 50 | 100 | 37 | 38 | 46 | 48 | 36.4 | 18.2 | 11.4 | 2.3 | 11122 | 11111 | 11111 | 11111 | 93 | 97 | 100 | 100 |
7B_S18 | AD-CAB_4007 | OA | 85 | bone | 7B_S18_L001_R1_001.fastq.gz | pvt | 72 | M | Yes | No | Anatomic | Right | 184.00 | 118.0 | 35.00 | 2 | Ever_smoker | No | Yes | Yes | No | 12.7 | 66 | 90 | 5.8 | 5.6 | 5.6 | Yes | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
7C_S32 | AD-CAB_4007 | OA | 85 | capsule | 7C_S32_L001_R1_001.fastq.gz | pvt | 72 | M | Yes | No | Anatomic | Right | 184.00 | 118.0 | 35.00 | 2 | Ever_smoker | No | Yes | Yes | No | 12.7 | 66 | 90 | 5.8 | 5.6 | 5.6 | Yes | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
7S_S46 | AD-CAB_4007 | OA | 85 | synovium | 7S_S46_L001_R1_001.fastq.gz | pvt | 72 | M | Yes | No | Anatomic | Right | 184.00 | 118.0 | 35.00 | 2 | Ever_smoker | No | Yes | Yes | No | 12.7 | 66 | 90 | 5.8 | 5.6 | 5.6 | Yes | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
8.1_S48 | AD-CAB_3008 | RC | 60 | capsule | 8-1_S48_L001_R1_001.fastq.gz | NA | 70 | M | NA | NA | NA | Left | 167.00 | 71.0 | 25.50 | 2 | Never_smoker | No | Yes | Yes | No | 2.9 | 87 | 77 | 7.3 | 5.5 | 5.4 | No | Intact | NA | NA | NA | 24 | 25 | 47 | NA | 54.5 | 54.5 | 11.4 | NA | 22221 | 22221 | 11111 | NA | 90 | 90 | 92 | NA |
8.2_S74 | AD-CAB_3008 | RC | 60 | tendon | 8-2_S74_L001_R1_001.fastq.gz | NA | 70 | M | NA | NA | NA | Left | 167.00 | 71.0 | 25.50 | 2 | Never_smoker | No | Yes | Yes | No | 2.9 | 87 | 77 | 7.3 | 5.5 | 5.4 | No | Intact | NA | NA | NA | 24 | 25 | 47 | NA | 54.5 | 54.5 | 11.4 | NA | 22221 | 22221 | 11111 | NA | 90 | 90 | 92 | NA |
8.3_S100 | AD-CAB_3008 | RC | 60 | tear | 8-3_S100_L001_R1_001.fastq.gz | NA | 70 | M | NA | NA | NA | Left | 167.00 | 71.0 | 25.50 | 2 | Never_smoker | No | Yes | Yes | No | 2.9 | 87 | 77 | 7.3 | 5.5 | 5.4 | No | Intact | NA | NA | NA | 24 | 25 | 47 | NA | 54.5 | 54.5 | 11.4 | NA | 22221 | 22221 | 11111 | NA | 90 | 90 | 92 | NA |
8B_S19 | AD-CAB_4008 | OA | 86 | bone | 8B_S19_L001_R1_001.fastq.gz | pub | 70 | M | Yes | No | Anatomic | Right | 172.00 | 86.0 | 29.00 | 2 | Never_smoker | No | No | Yes | No | 2.9 | 103 | 64 | 7.9 | 5.6 | 5.6 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
8C_S33 | AD-CAB_4008 | OA | 86 | capsule | 8C_S33_L001_R1_001.fastq.gz | pub | 70 | M | Yes | No | Anatomic | Right | 172.00 | 86.0 | 29.00 | 2 | Never_smoker | No | No | Yes | No | 2.9 | 103 | 64 | 7.9 | 5.6 | 5.6 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
8S_S47 | AD-CAB_4008 | OA | 86 | synovium | 8S_S47_L001_R1_001.fastq.gz | pub | 70 | M | Yes | No | Anatomic | Right | 172.00 | 86.0 | 29.00 | 2 | Never_smoker | No | No | Yes | No | 2.9 | 103 | 64 | 7.9 | 5.6 | 5.6 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
9.1_S49 | AD-CAB_3009 | RC | 61 | capsule | 9-1_S49_L001_R1_001.fastq.gz | NA | 68 | M | NA | NA | NA | Right | 182.00 | 83.0 | 25.10 | 2 | Ever_smoker | No | No | No | No | 2.9 | 79 | 88 | 7.5 | 5.8 | 5.8 | No | Intact | 50 | 50 | 100 | 35 | 41 | 43 | 46 | 52.3 | 11.4 | 4.5 | 2.3 | 11211 | 11121 | 11111 | 11111 | 85 | 96 | 90 | 90 |
9.2_S75 | AD-CAB_3009 | RC | 61 | tendon | 9-2_S75_L001_R1_001.fastq.gz | NA | 68 | M | NA | NA | NA | Right | 182.00 | 83.0 | 25.10 | 2 | Ever_smoker | No | No | No | No | 2.9 | 79 | 88 | 7.5 | 5.8 | 5.8 | No | Intact | 50 | 50 | 100 | 35 | 41 | 43 | 46 | 52.3 | 11.4 | 4.5 | 2.3 | 11211 | 11121 | 11111 | 11111 | 85 | 96 | 90 | 90 |
9.3_S101 | AD-CAB_3009 | RC | 61 | tear | 9-3_S101_L001_R1_001.fastq.gz | NA | 68 | M | NA | NA | NA | Right | 182.00 | 83.0 | 25.10 | 2 | Ever_smoker | No | No | No | No | 2.9 | 79 | 88 | 7.5 | 5.8 | 5.8 | No | Intact | 50 | 50 | 100 | 35 | 41 | 43 | 46 | 52.3 | 11.4 | 4.5 | 2.3 | 11211 | 11121 | 11111 | 11111 | 85 | 96 | 90 | 90 |
9B_S20 | AD-CAB_4009 | OA | 88 | bone | 9B_S20_L001_R1_001.fastq.gz | pvt | 72 | M | No | Yes | Reverse | Right | 167.00 | 80.0 | 29.00 | 3 | Ever_smoker | No | Yes | Yes | No | 2.9 | 107 | 59 | 6.7 | 5.8 | 5.5 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
9C_S34 | AD-CAB_4009 | OA | 88 | capsule | 9C_S34_L001_R1_001.fastq.gz | pvt | 72 | M | No | Yes | Reverse | Right | 167.00 | 80.0 | 29.00 | 3 | Ever_smoker | No | Yes | Yes | No | 2.9 | 107 | 59 | 6.7 | 5.8 | 5.5 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
9S_S48 | AD-CAB_4009 | OA | 88 | synovium | 9S_S48_L001_R1_001.fastq.gz | pvt | 72 | M | No | Yes | Reverse | Right | 167.00 | 80.0 | 29.00 | 3 | Ever_smoker | No | Yes | Yes | No | 2.9 | 107 | 59 | 6.7 | 5.8 | 5.5 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
SL2.08Re_S60 | AD-CAB_4014 | OA | 92 | bone | SL2-08Re_S60_L001_R1_001.fastq.gz | pvt | 71 | M | Yes | No | Reverse | Right | 170.00 | 99.0 | 34.00 | 2 | Ever_smoker | No | Yes | No | Yes | 2.9 | 69 | 90 | 7.0 | 7.0 | 7.1 | Yes | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
SM.027_S26 | AD-CAB_2001 | Insta | 27 | capsule | SM-027_S26_L001_R1_001.fastq.gz | pub | 18 | M | NA | NA | NA | Left | 188.00 | 80.0 | 22.60 | 2 | Ever_smoker | No | No | No | No | 5.2 | 87 | 90 | 3.9 | 4.9 | 5.4 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
SM.028_S27 | AD-CAB_2002 | Insta | 28 | capsule | SM-028_S27_L001_R1_001.fastq.gz | pub | 22 | F | NA | NA | NA | Right | 164.00 | 73.0 | 27.10 | 1 | Never_smoker | No | No | No | No | 2.9 | 58 | 90 | 3.6 | 3.4 | 4.8 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
SM.029_S28 | AD-CAB_2003 | Insta | 29 | capsule | SM-029_S28_L001_R1_001.fastq.gz | pvt | 21 | M | NA | NA | NA | Right | 178.00 | 105.0 | 33.00 | 1 | Ever_smoker | No | NA | No | Yes | 3.0 | 85 | 90 | 5.8 | 4.3 | 5.1 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
SM.030_S29 | AD-CAB_2004 | Insta | 30 | capsule | SM-030_S29_L001_R1_001.fastq.gz | pvt | 19 | M | NA | NA | NA | Left | 181.00 | 94.5 | 29.00 | 1 | Never_smoker | No | No | No | Normal | 2.9 | 69 | 90 | 5.7 | 4.8 | 5.4 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
SM.031_S30 | AD-CAB_2005 | Insta | 31 | capsule | SM-031_S30_L001_R1_001.fastq.gz | NA | 27 | M | NA | NA | NA | Right | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
SM.032_S31 | AD-CAB_2006 | Insta | 32 | capsule | SM-032_S31_L001_R1_001.fastq.gz | pub | 19 | F | NA | NA | NA | Left | 160.00 | 47.0 | 18.40 | 1 | Ever_smoker | No | No | No | No | 8.2 | 79 | 90 | 3.8 | 4.2 | 4.9 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
SM.033_S32 | AD-CAB_2007 | Insta | 33 | capsule | SM-033_S32_L001_R1_001.fastq.gz | pub | 18 | M | NA | NA | NA | Right | 180.00 | 74.0 | 22.80 | 1 | Never_smoker | No | NA | No | Yes | 2.9 | 81 | 90 | 5.5 | 6.6 | 4.9 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
SM.034_S33 | AD-CAB_2008 | Insta | 34 | capsule | SM-034_S33_L001_R1_001.fastq.gz | pub | 21 | M | NA | NA | NA | Right | 195.00 | 129.0 | 33.90 | 1 | Never_smoker | No | No | No | No | 2.9 | 96 | 90 | 5.9 | 4.9 | 4.7 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
SM.035_S34 | AD-CAB_2009 | Insta | 35 | capsule | SM-035_S34_L001_R1_001.fastq.gz | pub | 18 | M | NA | NA | NA | Right | 192.00 | 98.0 | 26.60 | 2 | Ever_smoker | No | No | No | No | 2.9 | 82 | 90 | 4.1 | 4.6 | 5.7 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
SM.036_S35 | AD-CAB_2010 | Insta | 36 | capsule | SM-036_S35_L001_R1_001.fastq.gz | pub | 21 | M | NA | NA | NA | Left | 180.00 | 115.0 | 35.50 | 2 | Ever_smoker | No | No | No | No | 3.2 | 84 | 90 | 5.4 | 4.4 | 5.3 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
SM.037_S36 | AD-CAB_2011 | Insta | 37 | capsule | SM-037_S36_L001_R1_001.fastq.gz | pub | 30 | M | NA | NA | NA | Left | 178.00 | 82.0 | 25.90 | 1 | Ever_smoker | No | No | No | No | 2.9 | 94 | 90 | 8.2 | 5.1 | 5.3 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
SM.038_S37 | AD-CAB_2012 | Insta | 38 | capsule | SM-038_S37_L001_R1_001.fastq.gz | pvt | 35 | M | NA | NA | NA | Left | 188.00 | 75.0 | 21.20 | 1 | Never_smoker | No | NA | No | No | 2.9 | 106 | 78 | 4.7 | 5.4 | 5.2 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
SM.039_S38 | AD-CAB_2013 | Insta | 39 | capsule | SM-039_S38_L001_R1_001.fastq.gz | pub | 21 | M | NA | NA | NA | Left | 175.00 | 96.0 | 31.30 | 1 | Never_smoker | No | No | No | No | NA | 93 | 90 | 4.1 | 4.6 | 4.9 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
SM.040_S39 | AD-CAB_2014 | Insta | 40 | capsule | SM-040_S39_L001_R1_001.fastq.gz | pub | 29 | M | NA | NA | NA | Right | 185.00 | 105.0 | 30.70 | 1 | Never_smoker | No | No | No | No | 2.9 | 81 | 90 | 6.5 | 5.0 | 4.6 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
SM.041_S40 | AD-CAB_2015 | Insta | 41 | capsule | SM-041_S40_L001_R1_001.fastq.gz | pub | 23 | M | NA | NA | NA | Left | 175.00 | 82.0 | 26.80 | 1 | Ever_smoker | No | No | No | No | 2.9 | 94 | 90 | 4.5 | 4.1 | 4.9 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
SM.042_S41 | AD-CAB_2016 | Insta | 42 | capsule | SM-042_S41_L001_R1_001.fastq.gz | pvt | 35 | M | NA | NA | NA | Right | 187.00 | 80.0 | 22.90 | 1 | Never_smoker | No | No | No | No | 2.9 | 103 | 81 | 4.9 | 4.5 | 5.0 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
SM.043_S42 | AD-CAB_2017 | Insta | 43 | capsule | SM-043_S42_L001_R1_001.fastq.gz | pub | 19 | M | NA | NA | NA | Right | 195.00 | 118.0 | 31.00 | 2 | Never_smoker | No | No | No | No | 2.9 | 95 | 90 | 6.2 | 4.2 | 4.5 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
SM.044_S43 | AD-CAB_2018 | Insta | 44 | capsule | SM-044_S43_L001_R1_001.fastq.gz | pub | 27 | M | NA | NA | NA | Right | 170.00 | 82.0 | 28.40 | 1 | Never_smoker | No | No | No | No | NA | 95 | 90 | 6.2 | 5.4 | 5.5 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
SM.045_S44 | AD-CAB_2019 | Insta | 45 | capsule | SM-045_S44_L001_R1_001.fastq.gz | pub | 27 | M | NA | NA | NA | Left | 180.00 | 76.0 | 23.50 | 1 | Ever_smoker | No | NA | No | No | 2.9 | 65 | 90 | 6.9 | 4.5 | 4.9 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
SM.046_S45 | AD-CAB_2020 | Insta | 46 | capsule | SM-046_S45_L001_R1_001.fastq.gz | pub | 20 | M | NA | NA | NA | Left | 181.00 | 85.0 | 25.90 | 1 | Never_smoker | No | No | No | No | 2.9 | 105 | 86 | 5.8 | 4.4 | 5.0 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
SM.047_S46 | AD-CAB_2021 | Insta | 47 | capsule | SM-047_S46_L001_R1_001.fastq.gz | pub | 18 | M | NA | NA | NA | Left | 176.00 | 65.0 | 21.00 | 1 | Never_smoker | No | No | No | No | 2.9 | 68 | 90 | 4.5 | 4.3 | 4.8 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
SM.048_S47 | AD-CAB_2022 | Insta | 48 | capsule | SM-048_S47_L001_R1_001.fastq.gz | pvt | 32 | F | NA | NA | NA | Left | 166.00 | 66.0 | 24.00 | 1 | Never_smoker | No | NA | No | Yes | 2.9 | 52 | 90 | 3.1 | 4.1 | 5.3 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
SM.049_S48 | AD-CAB_2023 | Insta | 49 | capsule | SM-049_S48_L001_R1_001.fastq.gz | pvt | 27 | F | NA | NA | NA | Left | 170.00 | 66.0 | 22.80 | 1 | Never_smoker | No | No | No | No | 2.9 | 91 | 75 | 5.5 | 4.3 | 4.9 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
SM.050_S49 | AD-CAB_2024 | Insta | 50 | capsule | SM-050_S49_L001_R1_001.fastq.gz | pvt | 21 | M | NA | NA | NA | Right | 189.00 | 83.0 | 23.20 | 1 | Never_smoker | No | NA | No | No | 2.9 | 87 | 90 | 3.9 | 4.7 | 4.9 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
SM.051_S50 | AD-CAB_2025 | Insta | 51 | capsule | SM-051_S50_L001_R1_001.fastq.gz | pvt | 21 | M | NA | NA | NA | Right | 173.00 | 92.0 | 31.00 | 1 | Ever_smoker | No | NA | No | No | 2.9 | 71 | 90 | 4.1 | 4.7 | 5.8 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
SM.052_S51 | AD-CAB_2026 | Insta | 52 | capsule | SM-052_S51_L001_R1_001.fastq.gz | pub | 23 | F | NA | NA | NA | Left | 169.00 | 57.0 | 20.00 | 2 | Ever_smoker | No | No | No | Yes | 2.9 | 68 | 90 | 4.5 | 4.6 | 5.1 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
Importing osteoarthritis (OA) and shoulder instability (SI) data separately. Aggregate Lanes together.
if ( !file.exists("counts.rds") ) {
tmp <- read.table("../fastq/3col.tsv.gz",header=F)
x <- as.matrix(acast(tmp, V2~V1, value.var="V3", fun.aggregate = sum))
x <- as.data.frame(x)
accession <- sapply((strsplit(rownames(x),"\\|")),"[[",2)
symbol<-sapply((strsplit(rownames(x),"\\|")),"[[",6)
x$geneid <- paste(accession,symbol)
xx <- aggregate(. ~ geneid,x,sum)
rownames(xx) <- xx$geneid
#colnames <- gsub("T0R","T0",colnames(xx))
xx$geneid = NULL
xx <- round(xx)
txx <- data.frame(t(xx))
txx$sample <- gsub("_L001","",rownames(txx))
txx$sample <- gsub("_L002","",txx$sample)
txx2 <- aggregate(. ~ sample,txx,sum)
rownames(txx2) <- txx2$sample
txx2$sample = NULL
axx <- data.frame(t(txx2))
axx <- axx[,order(colnames(axx))]
colnames(axx) <- gsub("^X","",colnames(axx))
axx <- axx[,order(colnames(axx))]
remove(tmp,x,xx,txx,txx2)
gc()
saveRDS(axx,"counts.rds")
} else {
axx <- readRDS("counts.rds")
}
Running some checks to ensure that the sample sheet matches the list of datasets.
message("Dimesions of sample sheet:")
## Dimesions of sample sheet:
dim(ss)
## [1] 165 48
message("Dimesions of count matrix:")
## Dimesions of count matrix:
dim(axx)
## [1] 60651 179
message("Number of duplicated samples in the count matrix:")
## Number of duplicated samples in the count matrix:
length(which(duplicated(colnames(axx))))
## [1] 0
message("sample sheet entries with matching datasets")
## sample sheet entries with matching datasets
length(which(rownames(ss) %in% colnames(axx)))
## [1] 165
message("datasets not found in sample sheet")
## datasets not found in sample sheet
colnames(axx)[!colnames(axx) %in% rownames(ss)]
## [1] "4001.41F" "4001.41M" "4002.42F" "4002.42M" "4003.43F"
## [6] "4003.43M" "4004.44F" "4004.44M" "4005.45F" "4005.45M"
## [11] "4006.46F" "4006.46M" "SL2.29Re_S61" "SL2.31Re_S62"
There are some datasets not included in the sample sheet so I will ask Sam to get those clinical data so they can be included in future.
Here I’ll look at a few different quality control measures.
par(mar=c(5,8,3,1))
barplot(colSums(axx),horiz=TRUE,las=1,xlab="OA num reads")
sums <- colSums(axx)
sums <- sums[order(sums)]
barplot(sums,horiz=TRUE,las=1,xlab="OA num reads")
abline(v=15000000,col="red")
Some of those read counts are quite low.
Multidimensional scaling plot to show the variation between all samples, very similar to PCA.
mds <- cmdscale(dist(t(axx)))
plot(mds, xlab="Coordinate 1", ylab="Coordinate 2",
type = "p",bty="n",pch=19, cex=4 ,col="gray")
text(mds, labels=rownames(mds) )
Need to:
select Cuff and OA samples
select bone datasets only
ss0 <- subset(ss,Cuff_Arthropathy=="Yes" | Primary_OA=="Yes")
ss0b <- subset(ss0,Tissue=="bone")
ss0b %>%
kbl(caption = "sample sheet for cuff arth vs OA (bone)") %>%
kable_paper("hover", full_width = F)
Participant_ID | Case | Redcap_ID | Tissue | fastq | pvt.pub | Age | Sex | Primary_OA | Cuff_Arthropathy | Prosthesis | Affected_Side | Height_cm | Weight_kg | BMI | ASA | Smoking | Diabetes | Hypercholesterolaemia | Hypertension | Thyroid | CRP | Creat | eGFR | Urea | Fast_Glucose | hba1c | Metabolic_Syndrome | Tendon_integrity_2_years_post.op | ASES_2_years_post.op_Pain | ASES_2_years_post.op_ADL | ASES_2_years_post.op_Total | Oxford_Baseline | Oxford_3_month | Oxford_12_month | Oxford_24_month | QuickDASH_ | QuickDASH_3_month | QuickDASH_12_month | QuickDASH_24_month | EQ.5D.3L_Baseline | EQ.5D.3L_3_month | EQ.5D.3L_12_month | EQ.5D.3L_24_month | EQVAS_Baseline | EQVAS_3_month | EQVAS_12_month | EQVAS_24_month | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
10B_S21 | AD-CAB_4010 | OA | 90 | bone | 10B_S21_L001_R1_001.fastq.gz | pvt | 80 | F | No | Yes | Reverse | Left | 161 | 72 | 28 | 2 | Never_smoker | No | Yes | No | Yes | 11.2 | 54 | 86 | 8.5 | 7.3 | 5.6 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
11B_S22 | AD-CAB_4011 | OA | 87 | bone | 11B_S22_L001_R1_001.fastq.gz | pub | 76 | M | Yes | No | Reverse | Right | 180 | 92 | 28 | 2 | Never_smoker | No | Yes | Yes | No | 4.0 | 75 | 85 | 7.0 | 6.0 | 6.0 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
12B_S23 | AD-CAB_4012 | OA | 91 | bone | 12B_S23_L001_R1_001.fastq.gz | pub | 71 | F | Yes | No | Anatomic | Right | 163 | 83 | 31 | 2 | Never_smoker | No | Yes | Yes | No | 2.9 | 73 | 72 | 4.8 | 6.3 | 5.7 | Yes | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
13B_S24 | AD-CAB_4013 | OA | 89 | bone | 13B_S24_L001_R1_001.fastq.gz | pvt | 69 | F | No | Yes | Reverse | Left | 170 | 89 | 31 | 2 | Never_smoker | No | Yes | Yes | No | 2.9 | 81 | 85 | 5.1 | 5.4 | 5.9 | Yes | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
14B_S25 | AD-CAB_4014 | OA | 92 | bone | 14B_S25_L001_R1_001.fastq.gz | pvt | 71 | M | Yes | No | Reverse | Right | 170 | 99 | 34 | 2 | Ever_smoker | No | Yes | No | Yes | 2.9 | 69 | 90 | 7.0 | 7.0 | 7.1 | Yes | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
15B_S26 | AD-CAB_4015 | OA | 93 | bone | 15B_S26_L001_R1_001.fastq.gz | pvt | 76 | M | Yes | No | Anatomic | Left | 183 | 95 | 28 | 2 | Ever_smoker | No | Yes | Yes | No | 5.6 | 90 | 71 | 6.6 | 5.5 | 5.0 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
16B_S27 | AD-CAB_4016 | OA | 99 | bone | 16B_S27_L001_R1_001.fastq.gz | pvt | 76 | F | Yes | No | Anatomic | Left | 167 | 54 | 19 | 3 | Ever_smoker | No | No | No | Yes | 2.9 | 60 | 86 | 11.0 | 4.7 | 5.3 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
17B_S28 | AD-CAB_4017 | OA | 96 | bone | 17B_S28_L001_R1_001.fastq.gz | pvt | 79 | F | Yes | No | Reverse | Right | 155 | 75 | 31 | 2 | Never_smoker | No | No | No | No | 9.2 | 71 | 70 | 4.5 | 5.5 | 5.1 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
18B_S29 | AD-CAB_4018 | OA | 97 | bone | 18B_S29_L001_R1_001.fastq.gz | pvt | 73 | F | Yes | No | Anatomic | Right | 167 | 85 | 30 | 3 | Ever_smoker | No | Yes | No | No | 1.5 | 78 | 65 | 7.3 | 5.4 | 5.9 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
19B_S30 | AD-CAB_4019 | OA | 95 | bone | 19B_S30_L001_R1_001.fastq.gz | pvt | 65 | F | Yes | No | Anatomic | Left | 170 | 62 | 21 | 2 | Never_smoker | No | No | Yes | No | 2.9 | 103 | 49 | 11.0 | 5.3 | 5.2 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
20B_S31 | AD-CAB_4020 | OA | 98 | bone | 20B_S31_L001_R1_001.fastq.gz | pvt | 62 | M | Yes | No | Anatomic | Left | 180 | 117 | 36 | 2 | Never_smoker | No | Yes | No | No | 2.9 | 80 | 90 | 4.9 | 6.9 | 5.9 | Yes | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
4001.41B | AD-CAB_4001 | OA | 84 | bone | 4001-41B_R1_001.fastq.gz | pvt | 69 | F | Yes | No | Anatomic | Left | 158 | 89 | 36 | 2 | Never_smoker | No | Yes | Yes | Yes | 2.9 | 66 | 82 | 5.2 | 5.7 | 6.1 | Yes | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
4002.42B | AD-CAB_4002 | OA | 80 | bone | 4002-42B_R1_001.fastq.gz | pvt | 59 | M | Yes | No | Anatomic | Left | 182 | 106 | 32 | 1 | Ever_smoker | No | Yes | No | No | 9.3 | 69 | 90 | 4.3 | 6.2 | 5.4 | Yes | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
4003.43B | AD-CAB_4003 | OA | 81 | bone | 4003-43B_R1_001.fastq.gz | pvt | 74 | F | No | Yes | Reverse | Right | 153 | 87 | 37 | 2 | Ever_smoker | No | Yes | Yes | No | 6.9 | 77 | 66 | 5.0 | 5.4 | 5.4 | Yes | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
4004.44B | AD-CAB_4004 | OA | 82 | bone | 4004-44B_R1_001.fastq.gz | pvt | 69 | F | Yes | No | Anatomic | Left | 165 | 85 | 32 | 2 | Never_smoker | No | Yes | Yes | Yes | 3.9 | 61 | 89 | 5.8 | 5.8 | 5.6 | Yes | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
4005.45B | AD-CAB_4005 | OA | 83 | bone | 4005-45B_R1_001.fastq.gz | pvt | 74 | F | Yes | No | Anatomic | Left | 169 | 75 | 26 | 2 | Ever_smoker | No | Yes | Yes | No | 2.9 | 90 | 72 | 6.6 | 5.2 | 5.7 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
4006.46B | AD-CAB_4006 | OA | 78 | bone | 4006-46B_R1_001.fastq.gz | pvt | 81 | F | Yes | No | Anatomic | Right | 150 | 54 | 24 | 3 | Never_smoker | No | Yes | Yes | No | 2.9 | 105 | 43 | 10.5 | 5.6 | 6.0 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
7B_S18 | AD-CAB_4007 | OA | 85 | bone | 7B_S18_L001_R1_001.fastq.gz | pvt | 72 | M | Yes | No | Anatomic | Right | 184 | 118 | 35 | 2 | Ever_smoker | No | Yes | Yes | No | 12.7 | 66 | 90 | 5.8 | 5.6 | 5.6 | Yes | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
8B_S19 | AD-CAB_4008 | OA | 86 | bone | 8B_S19_L001_R1_001.fastq.gz | pub | 70 | M | Yes | No | Anatomic | Right | 172 | 86 | 29 | 2 | Never_smoker | No | No | Yes | No | 2.9 | 103 | 64 | 7.9 | 5.6 | 5.6 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
9B_S20 | AD-CAB_4009 | OA | 88 | bone | 9B_S20_L001_R1_001.fastq.gz | pvt | 72 | M | No | Yes | Reverse | Right | 167 | 80 | 29 | 3 | Ever_smoker | No | Yes | Yes | No | 2.9 | 107 | 59 | 6.7 | 5.8 | 5.5 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
SL2.08Re_S60 | AD-CAB_4014 | OA | 92 | bone | SL2-08Re_S60_L001_R1_001.fastq.gz | pvt | 71 | M | Yes | No | Reverse | Right | 170 | 99 | 34 | 2 | Ever_smoker | No | Yes | No | Yes | 2.9 | 69 | 90 | 7.0 | 7.0 | 7.1 | Yes | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
message("Metabolic syndrome classification")
## Metabolic syndrome classification
ss0b$Metabolic_Syndrome
## [1] "No" "No" "Yes" "Yes" "Yes" "No" "No" "No" "No" "No" "Yes" "Yes"
## [13] "Yes" "Yes" "Yes" "No" "No" "Yes" "No" "No" "Yes"
message("Age data")
## Age data
ss0b$Age
## [1] 80 76 71 69 71 76 76 79 73 65 62 69 59 74 69 74 81 72 70 72 71
message("Sex data")
## Sex data
ss0b$Sex
## [1] "F" "M" "F" "F" "M" "M" "F" "F" "F" "F" "M" "F" "M" "F" "F" "F" "F" "M" "M"
## [20] "M" "M"
x0b <- axx[,colnames(axx) %in% rownames(ss0b)]
message("count matrix dimensions before filtering out low genes")
## count matrix dimensions before filtering out low genes
dim(x0b)
## [1] 60651 21
message("count matrix dimensions after filtering out low genes")
## count matrix dimensions after filtering out low genes
x0b <- x0b[which(rowMeans(x0b)>=10),]
dim(x0b)
## [1] 18383 21
x0b <- x0b[,order(colnames(x0b))]
ss0b <- ss0b[order(rownames(ss0b)),]
ss0b %>%
kbl(caption = "sample sheet") %>%
kable_paper("hover", full_width = F)
Participant_ID | Case | Redcap_ID | Tissue | fastq | pvt.pub | Age | Sex | Primary_OA | Cuff_Arthropathy | Prosthesis | Affected_Side | Height_cm | Weight_kg | BMI | ASA | Smoking | Diabetes | Hypercholesterolaemia | Hypertension | Thyroid | CRP | Creat | eGFR | Urea | Fast_Glucose | hba1c | Metabolic_Syndrome | Tendon_integrity_2_years_post.op | ASES_2_years_post.op_Pain | ASES_2_years_post.op_ADL | ASES_2_years_post.op_Total | Oxford_Baseline | Oxford_3_month | Oxford_12_month | Oxford_24_month | QuickDASH_ | QuickDASH_3_month | QuickDASH_12_month | QuickDASH_24_month | EQ.5D.3L_Baseline | EQ.5D.3L_3_month | EQ.5D.3L_12_month | EQ.5D.3L_24_month | EQVAS_Baseline | EQVAS_3_month | EQVAS_12_month | EQVAS_24_month | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
10B_S21 | AD-CAB_4010 | OA | 90 | bone | 10B_S21_L001_R1_001.fastq.gz | pvt | 80 | F | No | Yes | Reverse | Left | 161 | 72 | 28 | 2 | Never_smoker | No | Yes | No | Yes | 11.2 | 54 | 86 | 8.5 | 7.3 | 5.6 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
11B_S22 | AD-CAB_4011 | OA | 87 | bone | 11B_S22_L001_R1_001.fastq.gz | pub | 76 | M | Yes | No | Reverse | Right | 180 | 92 | 28 | 2 | Never_smoker | No | Yes | Yes | No | 4.0 | 75 | 85 | 7.0 | 6.0 | 6.0 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
12B_S23 | AD-CAB_4012 | OA | 91 | bone | 12B_S23_L001_R1_001.fastq.gz | pub | 71 | F | Yes | No | Anatomic | Right | 163 | 83 | 31 | 2 | Never_smoker | No | Yes | Yes | No | 2.9 | 73 | 72 | 4.8 | 6.3 | 5.7 | Yes | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
13B_S24 | AD-CAB_4013 | OA | 89 | bone | 13B_S24_L001_R1_001.fastq.gz | pvt | 69 | F | No | Yes | Reverse | Left | 170 | 89 | 31 | 2 | Never_smoker | No | Yes | Yes | No | 2.9 | 81 | 85 | 5.1 | 5.4 | 5.9 | Yes | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
14B_S25 | AD-CAB_4014 | OA | 92 | bone | 14B_S25_L001_R1_001.fastq.gz | pvt | 71 | M | Yes | No | Reverse | Right | 170 | 99 | 34 | 2 | Ever_smoker | No | Yes | No | Yes | 2.9 | 69 | 90 | 7.0 | 7.0 | 7.1 | Yes | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
15B_S26 | AD-CAB_4015 | OA | 93 | bone | 15B_S26_L001_R1_001.fastq.gz | pvt | 76 | M | Yes | No | Anatomic | Left | 183 | 95 | 28 | 2 | Ever_smoker | No | Yes | Yes | No | 5.6 | 90 | 71 | 6.6 | 5.5 | 5.0 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
16B_S27 | AD-CAB_4016 | OA | 99 | bone | 16B_S27_L001_R1_001.fastq.gz | pvt | 76 | F | Yes | No | Anatomic | Left | 167 | 54 | 19 | 3 | Ever_smoker | No | No | No | Yes | 2.9 | 60 | 86 | 11.0 | 4.7 | 5.3 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
17B_S28 | AD-CAB_4017 | OA | 96 | bone | 17B_S28_L001_R1_001.fastq.gz | pvt | 79 | F | Yes | No | Reverse | Right | 155 | 75 | 31 | 2 | Never_smoker | No | No | No | No | 9.2 | 71 | 70 | 4.5 | 5.5 | 5.1 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
18B_S29 | AD-CAB_4018 | OA | 97 | bone | 18B_S29_L001_R1_001.fastq.gz | pvt | 73 | F | Yes | No | Anatomic | Right | 167 | 85 | 30 | 3 | Ever_smoker | No | Yes | No | No | 1.5 | 78 | 65 | 7.3 | 5.4 | 5.9 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
19B_S30 | AD-CAB_4019 | OA | 95 | bone | 19B_S30_L001_R1_001.fastq.gz | pvt | 65 | F | Yes | No | Anatomic | Left | 170 | 62 | 21 | 2 | Never_smoker | No | No | Yes | No | 2.9 | 103 | 49 | 11.0 | 5.3 | 5.2 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
20B_S31 | AD-CAB_4020 | OA | 98 | bone | 20B_S31_L001_R1_001.fastq.gz | pvt | 62 | M | Yes | No | Anatomic | Left | 180 | 117 | 36 | 2 | Never_smoker | No | Yes | No | No | 2.9 | 80 | 90 | 4.9 | 6.9 | 5.9 | Yes | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
4001.41B | AD-CAB_4001 | OA | 84 | bone | 4001-41B_R1_001.fastq.gz | pvt | 69 | F | Yes | No | Anatomic | Left | 158 | 89 | 36 | 2 | Never_smoker | No | Yes | Yes | Yes | 2.9 | 66 | 82 | 5.2 | 5.7 | 6.1 | Yes | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
4002.42B | AD-CAB_4002 | OA | 80 | bone | 4002-42B_R1_001.fastq.gz | pvt | 59 | M | Yes | No | Anatomic | Left | 182 | 106 | 32 | 1 | Ever_smoker | No | Yes | No | No | 9.3 | 69 | 90 | 4.3 | 6.2 | 5.4 | Yes | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
4003.43B | AD-CAB_4003 | OA | 81 | bone | 4003-43B_R1_001.fastq.gz | pvt | 74 | F | No | Yes | Reverse | Right | 153 | 87 | 37 | 2 | Ever_smoker | No | Yes | Yes | No | 6.9 | 77 | 66 | 5.0 | 5.4 | 5.4 | Yes | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
4004.44B | AD-CAB_4004 | OA | 82 | bone | 4004-44B_R1_001.fastq.gz | pvt | 69 | F | Yes | No | Anatomic | Left | 165 | 85 | 32 | 2 | Never_smoker | No | Yes | Yes | Yes | 3.9 | 61 | 89 | 5.8 | 5.8 | 5.6 | Yes | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
4005.45B | AD-CAB_4005 | OA | 83 | bone | 4005-45B_R1_001.fastq.gz | pvt | 74 | F | Yes | No | Anatomic | Left | 169 | 75 | 26 | 2 | Ever_smoker | No | Yes | Yes | No | 2.9 | 90 | 72 | 6.6 | 5.2 | 5.7 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
4006.46B | AD-CAB_4006 | OA | 78 | bone | 4006-46B_R1_001.fastq.gz | pvt | 81 | F | Yes | No | Anatomic | Right | 150 | 54 | 24 | 3 | Never_smoker | No | Yes | Yes | No | 2.9 | 105 | 43 | 10.5 | 5.6 | 6.0 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
7B_S18 | AD-CAB_4007 | OA | 85 | bone | 7B_S18_L001_R1_001.fastq.gz | pvt | 72 | M | Yes | No | Anatomic | Right | 184 | 118 | 35 | 2 | Ever_smoker | No | Yes | Yes | No | 12.7 | 66 | 90 | 5.8 | 5.6 | 5.6 | Yes | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
8B_S19 | AD-CAB_4008 | OA | 86 | bone | 8B_S19_L001_R1_001.fastq.gz | pub | 70 | M | Yes | No | Anatomic | Right | 172 | 86 | 29 | 2 | Never_smoker | No | No | Yes | No | 2.9 | 103 | 64 | 7.9 | 5.6 | 5.6 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
9B_S20 | AD-CAB_4009 | OA | 88 | bone | 9B_S20_L001_R1_001.fastq.gz | pvt | 72 | M | No | Yes | Reverse | Right | 167 | 80 | 29 | 3 | Ever_smoker | No | Yes | Yes | No | 2.9 | 107 | 59 | 6.7 | 5.8 | 5.5 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
SL2.08Re_S60 | AD-CAB_4014 | OA | 92 | bone | SL2-08Re_S60_L001_R1_001.fastq.gz | pvt | 71 | M | Yes | No | Reverse | Right | 170 | 99 | 34 | 2 | Ever_smoker | No | Yes | No | Yes | 2.9 | 69 | 90 | 7.0 | 7.0 | 7.1 | Yes | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
plotMDS(x0b)
message("here is the model spec:")
## here is the model spec:
dds <- DESeqDataSetFromMatrix(countData = x0b , colData = ss0b, design = ~ Primary_OA)
## converting counts to integer mode
## Warning in DESeqDataSet(se, design = design, ignoreRank): some variables in
## design formula are characters, converting to factors
res <- DESeq(dds)
## estimating size factors
## estimating dispersions
## gene-wise dispersion estimates
## mean-dispersion relationship
## final dispersion estimates
## fitting model and testing
## -- replacing outliers and refitting for 352 genes
## -- DESeq argument 'minReplicatesForReplace' = 7
## -- original counts are preserved in counts(dds)
## estimating dispersions
## fitting model and testing
z<- results(res)
vsd <- vst(dds, blind=FALSE)
zz <- cbind(as.data.frame(z),assay(vsd))
dge <- as.data.frame(zz[order(zz$pvalue),])
dge[1:20,1:6] %>%
kbl(caption = "Top DEGs in bone between cuff arthropathy and OA patients (not correcting for age and sex)") %>%
kable_paper("hover", full_width = F)
baseMean | log2FoldChange | lfcSE | stat | pvalue | padj | |
---|---|---|---|---|---|---|
ENSG00000231475.3.IGHV4.31 | 113.354037 | 6.9274367 | 1.3009571 | 5.324877 | 0.0000001 | 0.0018396 |
ENSG00000160221.18.GATD3A | 70.673997 | -3.0178695 | 0.5807588 | -5.196425 | 0.0000002 | 0.0018498 |
ENSG00000226065.1.ZBTB45P2 | 13.633349 | 5.6825934 | 1.2070574 | 4.707807 | 0.0000025 | 0.0151990 |
ENSG00000231187.3.AL356056.2 | 11.902012 | 5.4870840 | 1.1911387 | 4.606587 | 0.0000041 | 0.0186349 |
ENSG00000184923.12.NUTM2A | 20.418626 | 3.8952646 | 0.9541063 | 4.082632 | 0.0000445 | 0.1050535 |
ENSG00000204176.14.SYT15 | 59.723331 | 1.4876952 | 0.3645375 | 4.081049 | 0.0000448 | 0.1050535 |
ENSG00000237541.4.HLA.DQA2 | 102.838822 | 3.4494118 | 0.8453578 | 4.080416 | 0.0000450 | 0.1050535 |
ENSG00000233937.7.CTC.338M12.4 | 33.402510 | 2.1079769 | 0.5222860 | 4.036059 | 0.0000544 | 0.1050535 |
ENSG00000280071.4.GATD3B | 437.645856 | 0.7596460 | 0.1882586 | 4.035120 | 0.0000546 | 0.1050535 |
ENSG00000109063.15.MYH3 | 43.805709 | 1.1627971 | 0.2891045 | 4.022066 | 0.0000577 | 0.1050535 |
ENSG00000115128.7.SF3B6 | 289.582072 | -0.9178741 | 0.2328682 | -3.941604 | 0.0000809 | 0.1339901 |
ENSG00000254395.1.IGHV4.55 | 72.919096 | 3.6203414 | 0.9264473 | 3.907768 | 0.0000932 | 0.1413590 |
ENSG00000279873.2.LINC01126 | 9.619567 | 3.1775559 | 0.8260587 | 3.846647 | 0.0001197 | 0.1581870 |
ENSG00000229391.7.HLA.DRB6 | 26.108495 | 3.1380284 | 0.8165895 | 3.842847 | 0.0001216 | 0.1581870 |
ENSG00000152380.10.FAM151B | 26.094286 | -1.0863202 | 0.2952610 | -3.679186 | 0.0002340 | 0.2667778 |
ENSG00000083099.11.LYRM2 | 158.613971 | -0.7606543 | 0.2070305 | -3.674117 | 0.0002387 | 0.2667778 |
ENSG00000275464.5.FP565260.1 | 152.484720 | 1.1697572 | 0.3206695 | 3.647859 | 0.0002644 | 0.2667778 |
ENSG00000105258.9.POLR2I | 111.099706 | -0.7580720 | 0.2085126 | -3.635616 | 0.0002773 | 0.2667778 |
ENSG00000242861.1.AL591895.1 | 22.734813 | 1.7209944 | 0.4749699 | 3.623376 | 0.0002908 | 0.2667778 |
ENSG00000169288.18.MRPL1 | 118.368539 | -1.1394894 | 0.3172411 | -3.591872 | 0.0003283 | 0.2667778 |
message("here is the model spec:")
## here is the model spec:
dds <- DESeqDataSetFromMatrix(countData = x0b , colData = ss0b, design = ~ Age + Sex + CRP + Primary_OA )
## converting counts to integer mode
## Warning in DESeqDataSet(se, design = design, ignoreRank): some variables in
## design formula are characters, converting to factors
## the design formula contains one or more numeric variables with integer values,
## specifying a model with increasing fold change for higher values.
## did you mean for this to be a factor? if so, first convert
## this variable to a factor using the factor() function
## the design formula contains one or more numeric variables that have mean or
## standard deviation larger than 5 (an arbitrary threshold to trigger this message).
## Including numeric variables with large mean can induce collinearity with the intercept.
## Users should center and scale numeric variables in the design to improve GLM convergence.
res <- DESeq(dds)
## estimating size factors
## estimating dispersions
## gene-wise dispersion estimates
## mean-dispersion relationship
## final dispersion estimates
## fitting model and testing
## 2 rows did not converge in beta, labelled in mcols(object)$betaConv. Use larger maxit argument with nbinomWaldTest
z<- results(res)
vsd <- vst(dds, blind=FALSE)
zz <- cbind(as.data.frame(z),assay(vsd))
dge <- as.data.frame(zz[order(zz$pvalue),])
dge[1:20,1:6] %>%
kbl(caption = "Top DEGs in bone between cuff arthropathy and OA patients adjusted for age, sex and CRP.") %>%
kable_paper("hover", full_width = F)
baseMean | log2FoldChange | lfcSE | stat | pvalue | padj | |
---|---|---|---|---|---|---|
ENSG00000231475.3.IGHV4.31 | 113.35404 | 7.691303 | 1.3877002 | 5.542482 | 0.00e+00 | 0.0005410 |
ENSG00000280411.1.IGHV1.69D | 352.87638 | 4.073358 | 0.7512319 | 5.422238 | 1.00e-07 | 0.0005410 |
ENSG00000160221.18.GATD3A | 70.67400 | -3.070696 | 0.5790845 | -5.302673 | 1.00e-07 | 0.0006993 |
ENSG00000261796.1.ISY1.RAB43 | 122.47263 | 2.575174 | 0.5688546 | 4.526946 | 6.00e-06 | 0.0244115 |
ENSG00000211966.2.IGHV5.51 | 379.90156 | 4.437549 | 0.9857874 | 4.501528 | 6.70e-06 | 0.0244115 |
ENSG00000226065.1.ZBTB45P2 | 13.63335 | 5.661125 | 1.2688283 | 4.461695 | 8.10e-06 | 0.0244115 |
ENSG00000280071.4.GATD3B | 437.64586 | 0.842649 | 0.1920091 | 4.388589 | 1.14e-05 | 0.0244115 |
ENSG00000270550.1.IGHV3.30 | 929.74531 | 3.974320 | 0.9076084 | 4.378893 | 1.19e-05 | 0.0244115 |
ENSG00000231187.3.AL356056.2 | 11.90201 | 5.391960 | 1.2314707 | 4.378472 | 1.20e-05 | 0.0244115 |
ENSG00000167476.10.JSRP1 | 69.52245 | 2.933264 | 0.6760584 | 4.338774 | 1.43e-05 | 0.0263392 |
ENSG00000211970.3.IGHV4.61 | 204.01512 | 4.750504 | 1.1310090 | 4.200235 | 2.67e-05 | 0.0445601 |
ENSG00000211951.2.IGHV2.26 | 54.88153 | 4.409251 | 1.0601240 | 4.159184 | 3.19e-05 | 0.0473066 |
ENSG00000236778.8.INTS6.AS1 | 53.12222 | -1.213004 | 0.2923899 | -4.148582 | 3.35e-05 | 0.0473066 |
ENSG00000237541.4.HLA.DQA2 | 102.83882 | 3.544540 | 0.8638749 | 4.103071 | 4.08e-05 | 0.0535342 |
ENSG00000206341.7.HLA.H | 42.42260 | 2.875753 | 0.7047631 | 4.080453 | 4.49e-05 | 0.0550853 |
ENSG00000228049.7.POLR2J2 | 30.45304 | 2.618078 | 0.6458746 | 4.053539 | 5.04e-05 | 0.0579623 |
ENSG00000211962.2.IGHV1.46 | 159.03236 | 3.745839 | 0.9313057 | 4.022138 | 5.77e-05 | 0.0623642 |
ENSG00000254395.1.IGHV4.55 | 72.91910 | 3.875863 | 0.9673194 | 4.006808 | 6.15e-05 | 0.0628543 |
ENSG00000211945.2.IGHV1.18 | 237.89449 | 4.064690 | 1.0220687 | 3.976924 | 6.98e-05 | 0.0643239 |
ENSG00000184923.12.NUTM2A | 20.41863 | 4.137140 | 1.0404372 | 3.976347 | 7.00e-05 | 0.0643239 |
dge0b <- dge
maplot(dge0b,"cuff arthropathy vs OA in bone")
make_volcano(dge0b,"cuff arthropathy vs OA in bone")
make_heatmap(dge0b,"cuff arthropathy vs OA in bone",groups=as.numeric(factor(ss0b$Primary_OA)),x0b,n=50)
Now for cuff arthropathy vs OA in capsule.
ss0 <- subset(ss,Cuff_Arthropathy=="Yes" | Primary_OA=="Yes")
ss0c <- subset(ss0,Tissue=="capsule")
ss0c %>%
kbl(caption = "sample sheet for cuff arth vs OA (capsule)") %>%
kable_paper("hover", full_width = F)
Participant_ID | Case | Redcap_ID | Tissue | fastq | pvt.pub | Age | Sex | Primary_OA | Cuff_Arthropathy | Prosthesis | Affected_Side | Height_cm | Weight_kg | BMI | ASA | Smoking | Diabetes | Hypercholesterolaemia | Hypertension | Thyroid | CRP | Creat | eGFR | Urea | Fast_Glucose | hba1c | Metabolic_Syndrome | Tendon_integrity_2_years_post.op | ASES_2_years_post.op_Pain | ASES_2_years_post.op_ADL | ASES_2_years_post.op_Total | Oxford_Baseline | Oxford_3_month | Oxford_12_month | Oxford_24_month | QuickDASH_ | QuickDASH_3_month | QuickDASH_12_month | QuickDASH_24_month | EQ.5D.3L_Baseline | EQ.5D.3L_3_month | EQ.5D.3L_12_month | EQ.5D.3L_24_month | EQVAS_Baseline | EQVAS_3_month | EQVAS_12_month | EQVAS_24_month | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
10C_S35 | AD-CAB_4010 | OA | 90 | capsule | 10C_S35_L001_R1_001.fastq.gz | pvt | 80 | F | No | Yes | Reverse | Left | 161 | 72 | 28 | 2 | Never_smoker | No | Yes | No | Yes | 11.2 | 54 | 86 | 8.5 | 7.3 | 5.6 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
11C_S36 | AD-CAB_4011 | OA | 87 | capsule | 11C_S36_L001_R1_001.fastq.gz | pub | 76 | M | No | Yes | Reverse | Right | 180 | 92 | 28 | 2 | Never_smoker | No | Yes | Yes | No | 4.0 | 75 | 85 | 7.0 | 6.0 | 6.0 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
12C_S37 | AD-CAB_4012 | OA | 91 | capsule | 12C_S37_L001_R1_001.fastq.gz | pub | 71 | F | Yes | No | Anatomic | Right | 163 | 83 | 31 | 2 | Never_smoker | No | Yes | Yes | No | 2.9 | 73 | 72 | 4.8 | 6.3 | 5.7 | Yes | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
13C_S38 | AD-CAB_4013 | OA | 89 | capsule | 13C_S38_L001_R1_001.fastq.gz | pvt | 69 | F | No | Yes | Reverse | Left | 170 | 89 | 31 | 2 | Never_smoker | No | Yes | Yes | No | 2.9 | 81 | 85 | 5.1 | 5.4 | 5.9 | Yes | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
14C_S39 | AD-CAB_4014 | OA | 92 | capsule | 14C_S39_L001_R1_001.fastq.gz | pvt | 71 | M | No | Yes | Reverse | Right | 170 | 99 | 34 | 2 | Ever_smoker | No | Yes | No | Yes | 2.9 | 69 | 90 | 7.0 | 7.0 | 7.1 | Yes | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
15C_S40 | AD-CAB_4015 | OA | 93 | capsule | 15C_S40_L001_R1_001.fastq.gz | pvt | 76 | M | Yes | No | Anatomic | Left | 183 | 95 | 28 | 2 | Ever_smoker | No | Yes | Yes | No | 5.6 | 90 | 71 | 6.6 | 5.5 | 5.0 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
16C_S41 | AD-CAB_4016 | OA | 99 | capsule | 16C_S41_L001_R1_001.fastq.gz | pvt | 76 | F | Yes | No | Anatomic | Left | 167 | 54 | 19 | 3 | Ever_smoker | No | No | No | Yes | 2.9 | 60 | 86 | 11.0 | 4.7 | 5.3 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
17C_S42 | AD-CAB_4017 | OA | 96 | capsule | 17C_S42_L001_R1_001.fastq.gz | pvt | 79 | F | No | Yes | Reverse | Right | 155 | 75 | 31 | 2 | Never_smoker | No | No | No | No | 9.2 | 71 | 70 | 4.5 | 5.5 | 5.1 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
18C_S43 | AD-CAB_4018 | OA | 97 | capsule | 18C_S43_L001_R1_001.fastq.gz | pvt | 73 | F | Yes | No | Anatomic | Right | 167 | 85 | 30 | 3 | Ever_smoker | No | Yes | No | No | 1.5 | 78 | 65 | 7.3 | 5.4 | 5.9 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
19C_S44 | AD-CAB_4019 | OA | 95 | capsule | 19C_S44_L001_R1_001.fastq.gz | pvt | 65 | F | Yes | No | Anatomic | Left | 170 | 62 | 21 | 2 | Never_smoker | No | No | Yes | No | 2.9 | 103 | 49 | 11.0 | 5.3 | 5.2 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
20C_S45 | AD-CAB_4020 | OA | 98 | capsule | 20C_S45_L001_R1_001.fastq.gz | pvt | 62 | M | Yes | No | Anatomic | Left | 180 | 117 | 36 | 2 | Never_smoker | No | Yes | No | No | 2.9 | 80 | 90 | 4.9 | 6.9 | 5.9 | Yes | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
4001.41C | AD-CAB_4001 | OA | 84 | capsule | 4001-41C_R1_001.fastq.gz | pvt | 69 | F | Yes | No | Anatomic | Left | 158 | 89 | 36 | 2 | Never_smoker | No | Yes | Yes | Yes | 2.9 | 66 | 82 | 5.2 | 5.7 | 6.1 | Yes | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
4002.42C | AD-CAB_4002 | OA | 80 | capsule | 4002-42C_R1_001.fastq.gz | pvt | 59 | M | Yes | No | Anatomic | Left | 182 | 106 | 32 | 1 | Ever_smoker | No | Yes | No | No | 9.3 | 69 | 90 | 4.3 | 6.2 | 5.4 | Yes | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
4003.43C | AD-CAB_4003 | OA | 81 | capsule | 4003-43C_R1_001.fastq.gz | pvt | 74 | F | No | Yes | Reverse | Right | 153 | 87 | 37 | 2 | Ever_smoker | No | Yes | Yes | No | 6.9 | 77 | 66 | 5.0 | 5.4 | 5.4 | Yes | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
4004.44C | AD-CAB_4004 | OA | 82 | capsule | 4004-44C_R1_001.fastq.gz | pvt | 69 | F | Yes | No | Anatomic | Left | 165 | 85 | 32 | 2 | Never_smoker | No | Yes | Yes | Yes | 3.9 | 61 | 89 | 5.8 | 5.8 | 5.6 | Yes | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
4005.45C | AD-CAB_4005 | OA | 83 | capsule | 4005-45C_R1_001.fastq.gz | pvt | 74 | F | Yes | No | Anatomic | Left | 169 | 75 | 26 | 2 | Ever_smoker | No | Yes | Yes | No | 2.9 | 90 | 72 | 6.6 | 5.2 | 5.7 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
4006.46C | AD-CAB_4006 | OA | 78 | capsule | 4006-46C_R1_001.fastq.gz | pvt | 81 | F | Yes | No | Anatomic | Right | 150 | 54 | 24 | 3 | Never_smoker | No | Yes | Yes | No | 2.9 | 105 | 43 | 10.5 | 5.6 | 6.0 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
7C_S32 | AD-CAB_4007 | OA | 85 | capsule | 7C_S32_L001_R1_001.fastq.gz | pvt | 72 | M | Yes | No | Anatomic | Right | 184 | 118 | 35 | 2 | Ever_smoker | No | Yes | Yes | No | 12.7 | 66 | 90 | 5.8 | 5.6 | 5.6 | Yes | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
8C_S33 | AD-CAB_4008 | OA | 86 | capsule | 8C_S33_L001_R1_001.fastq.gz | pub | 70 | M | Yes | No | Anatomic | Right | 172 | 86 | 29 | 2 | Never_smoker | No | No | Yes | No | 2.9 | 103 | 64 | 7.9 | 5.6 | 5.6 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
9C_S34 | AD-CAB_4009 | OA | 88 | capsule | 9C_S34_L001_R1_001.fastq.gz | pvt | 72 | M | No | Yes | Reverse | Right | 167 | 80 | 29 | 3 | Ever_smoker | No | Yes | Yes | No | 2.9 | 107 | 59 | 6.7 | 5.8 | 5.5 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
message("Metabolic syndrome classification")
## Metabolic syndrome classification
ss0c$Metabolic_Syndrome
## [1] "No" "No" "Yes" "Yes" "Yes" "No" "No" "No" "No" "No" "Yes" "Yes"
## [13] "Yes" "Yes" "Yes" "No" "No" "Yes" "No" "No"
message("Age data")
## Age data
ss0c$Age
## [1] 80 76 71 69 71 76 76 79 73 65 62 69 59 74 69 74 81 72 70 72
message("Sex data")
## Sex data
ss0c$Sex
## [1] "F" "M" "F" "F" "M" "M" "F" "F" "F" "F" "M" "F" "M" "F" "F" "F" "F" "M" "M"
## [20] "M"
x0c <- axx[,colnames(axx) %in% rownames(ss0c)]
message("count matrix dimensions before filtering out low genes")
## count matrix dimensions before filtering out low genes
dim(x0c)
## [1] 60651 20
x0c <- x0c[which(rowMeans(x0c)>=10),]
message("count matrix dimensions after filtering out low genes")
## count matrix dimensions after filtering out low genes
dim(x0c)
## [1] 17340 20
x0c <- x0c[,order(colnames(x0c))]
ss0c <- ss0c[order(rownames(ss0c)),]
plotMDS(x0c)
message("here is the model spec:")
## here is the model spec:
dds <- DESeqDataSetFromMatrix(countData = x0c , colData = ss0c, design = ~ Primary_OA)
## converting counts to integer mode
## Warning in DESeqDataSet(se, design = design, ignoreRank): some variables in
## design formula are characters, converting to factors
res <- DESeq(dds)
## estimating size factors
## estimating dispersions
## gene-wise dispersion estimates
## mean-dispersion relationship
## final dispersion estimates
## fitting model and testing
## -- replacing outliers and refitting for 94 genes
## -- DESeq argument 'minReplicatesForReplace' = 7
## -- original counts are preserved in counts(dds)
## estimating dispersions
## fitting model and testing
z<- results(res)
vsd <- vst(dds, blind=FALSE)
zz <- cbind(as.data.frame(z),assay(vsd))
dge <- as.data.frame(zz[order(zz$pvalue),])
dge[1:20,1:6] %>%
kbl(caption = "Top DEGs in bone between cuff arthropathy and OA patients (not correcting for age and sex)") %>%
kable_paper("hover", full_width = F)
baseMean | log2FoldChange | lfcSE | stat | pvalue | padj | |
---|---|---|---|---|---|---|
ENSG00000160221.18.GATD3A | 82.776968 | -2.6902133 | 0.4897308 | -5.493249 | 0.0000000 | 0.0006842 |
ENSG00000175084.12.DES | 130.464566 | 1.9970130 | 0.4913189 | 4.064596 | 0.0000481 | 0.3768375 |
ENSG00000241322.11.CDRT1 | 12.715250 | -1.9852864 | 0.5046605 | -3.933905 | 0.0000836 | 0.3768375 |
ENSG00000179935.10.LINC00652 | 14.262009 | -1.4152755 | 0.3693240 | -3.832070 | 0.0001271 | 0.3768375 |
ENSG00000114854.8.TNNC1 | 33.941783 | 2.9962035 | 0.7880244 | 3.802171 | 0.0001434 | 0.3768375 |
ENSG00000205054.8.LINC01121 | 10.112682 | -1.6777326 | 0.4518356 | -3.713148 | 0.0002047 | 0.3768375 |
ENSG00000261776.1.AC079414.2 | 15.868365 | -2.4479813 | 0.6642446 | -3.685361 | 0.0002284 | 0.3768375 |
ENSG00000197124.12.ZNF682 | 30.667027 | 1.1089760 | 0.3009262 | 3.685209 | 0.0002285 | 0.3768375 |
ENSG00000002745.13.WNT16 | 38.834851 | -4.2622131 | 1.1573304 | -3.682797 | 0.0002307 | 0.3768375 |
ENSG00000125912.11.NCLN | 430.132352 | 0.3500618 | 0.0969839 | 3.609483 | 0.0003068 | 0.3768375 |
ENSG00000133063.16.CHIT1 | 41.560145 | -2.0428240 | 0.5659999 | -3.609230 | 0.0003071 | 0.3768375 |
ENSG00000135127.11.BICDL1 | 17.614776 | -1.4165583 | 0.3939113 | -3.596135 | 0.0003230 | 0.3768375 |
ENSG00000135622.13.SEMA4F | 116.995538 | 0.5513237 | 0.1535505 | 3.590505 | 0.0003300 | 0.3768375 |
ENSG00000255458.7.AC108471.2 | 11.769050 | -1.8054217 | 0.5029325 | -3.589789 | 0.0003309 | 0.3768375 |
ENSG00000248144.6.ADH1C | 20.718223 | 2.7621798 | 0.7696270 | 3.588985 | 0.0003320 | 0.3768375 |
ENSG00000151338.18.MIPOL1 | 46.069885 | -0.9191058 | 0.2576117 | -3.567795 | 0.0003600 | 0.3768375 |
ENSG00000199753.1.SNORD104 | 22.793485 | 1.0002137 | 0.2835392 | 3.527602 | 0.0004193 | 0.3768375 |
ENSG00000154645.14.CHODL | 9.613827 | -3.2310250 | 0.9205096 | -3.510039 | 0.0004480 | 0.3768375 |
ENSG00000183054.12.RGPD6 | 102.597304 | 2.1690933 | 0.6180938 | 3.509327 | 0.0004492 | 0.3768375 |
ENSG00000163607.17.GTPBP8 | 53.948796 | -0.5705045 | 0.1629093 | -3.501976 | 0.0004618 | 0.3768375 |
message("here is the model spec:")
## here is the model spec:
dds <- DESeqDataSetFromMatrix(countData = x0c , colData = ss0c, design = ~ Age + Sex + CRP + Primary_OA )
## converting counts to integer mode
## Warning in DESeqDataSet(se, design = design, ignoreRank): some variables in
## design formula are characters, converting to factors
## the design formula contains one or more numeric variables with integer values,
## specifying a model with increasing fold change for higher values.
## did you mean for this to be a factor? if so, first convert
## this variable to a factor using the factor() function
## the design formula contains one or more numeric variables that have mean or
## standard deviation larger than 5 (an arbitrary threshold to trigger this message).
## Including numeric variables with large mean can induce collinearity with the intercept.
## Users should center and scale numeric variables in the design to improve GLM convergence.
res <- DESeq(dds)
## estimating size factors
## estimating dispersions
## gene-wise dispersion estimates
## mean-dispersion relationship
## final dispersion estimates
## fitting model and testing
## 2 rows did not converge in beta, labelled in mcols(object)$betaConv. Use larger maxit argument with nbinomWaldTest
z<- results(res)
vsd <- vst(dds, blind=FALSE)
zz <- cbind(as.data.frame(z),assay(vsd))
dge <- as.data.frame(zz[order(zz$pvalue),])
dge[1:20,1:6] %>%
kbl(caption = "Top DEGs in bone between cuff arthropathy and OA patients adjusted for age, sex and CRP.") %>%
kable_paper("hover", full_width = F)
baseMean | log2FoldChange | lfcSE | stat | pvalue | padj | |
---|---|---|---|---|---|---|
ENSG00000160221.18.GATD3A | 82.77697 | -2.8201856 | 0.5165101 | -5.460079 | 0.0000000 | 0.0008253 |
ENSG00000241322.11.CDRT1 | 12.71525 | -2.2904291 | 0.5623498 | -4.072961 | 0.0000464 | 0.2588321 |
ENSG00000261776.1.AC079414.2 | 15.86836 | -2.8887873 | 0.7313977 | -3.949681 | 0.0000783 | 0.2588321 |
ENSG00000175084.12.DES | 130.46457 | 1.8294800 | 0.4644204 | 3.939276 | 0.0000817 | 0.2588321 |
ENSG00000284722.2.AP003175.1 | 14.98458 | -2.2330722 | 0.5694452 | -3.921487 | 0.0000880 | 0.2588321 |
ENSG00000239704.11.CDRT4 | 71.06216 | 0.9557273 | 0.2448747 | 3.902924 | 0.0000950 | 0.2588321 |
ENSG00000255458.7.AC108471.2 | 11.76905 | -2.0403979 | 0.5258858 | -3.879926 | 0.0001045 | 0.2588321 |
ENSG00000130368.7.MAS1 | 20.09030 | -2.3785438 | 0.6225289 | -3.820776 | 0.0001330 | 0.2883475 |
ENSG00000269600.2.AC016629.2 | 17.06060 | -1.8487647 | 0.5015056 | -3.686428 | 0.0002274 | 0.3150250 |
ENSG00000005187.12.ACSM3 | 19.13072 | -1.7109043 | 0.4642966 | -3.684938 | 0.0002288 | 0.3150250 |
ENSG00000244040.7.IL12A.AS1 | 12.56259 | -2.2720054 | 0.6236527 | -3.643062 | 0.0002694 | 0.3150250 |
ENSG00000205930.10.C21orf62.AS1 | 41.39002 | -1.3878887 | 0.3838506 | -3.615700 | 0.0002995 | 0.3150250 |
ENSG00000205054.8.LINC01121 | 10.11268 | -1.8717111 | 0.5179307 | -3.613825 | 0.0003017 | 0.3150250 |
ENSG00000279085.1.AL022323.2 | 16.16489 | -2.3579100 | 0.6532940 | -3.609263 | 0.0003071 | 0.3150250 |
ENSG00000244128.7.LINC01322 | 19.80602 | -2.7691623 | 0.7686080 | -3.602828 | 0.0003148 | 0.3150250 |
ENSG00000261052.6.SULT1A3 | 152.76977 | 1.2454267 | 0.3457351 | 3.602257 | 0.0003155 | 0.3150250 |
ENSG00000260876.6.LINC01229 | 11.75654 | -1.5291981 | 0.4251893 | -3.596511 | 0.0003225 | 0.3150250 |
ENSG00000224810.1.AL355482.1 | 19.28433 | -2.2142403 | 0.6163669 | -3.592406 | 0.0003276 | 0.3150250 |
ENSG00000002745.13.WNT16 | 38.83485 | -3.6505808 | 1.0233230 | -3.567379 | 0.0003606 | 0.3150250 |
ENSG00000280071.4.GATD3B | 468.23472 | 0.6112931 | 0.1714532 | 3.565365 | 0.0003634 | 0.3150250 |
dge0c <- dge
maplot(dge0c,"cuff arthropathy vs OA in capsule")
make_volcano(dge0c,"cuff arthropathy vs OA in capsule")
make_heatmap(dge0c,"cuff arthropathy vs OA in capsule",groups=as.numeric(factor(ss0b$Primary_OA)),x0b,n=50)
Need to:
select bone datasets only
select OA samples only
look at the effect of metabolic syndrome in OA (ss1).
ss1 <- subset(ss,Primary_OA=="Yes")
ss1b <- subset(ss1,Tissue=="bone")
message("Metabolic syndrome classification")
## Metabolic syndrome classification
ss1b$Metabolic_Syndrome
## [1] "No" "Yes" "Yes" "No" "No" "No" "No" "No" "Yes" "Yes" "Yes" "Yes"
## [13] "No" "No" "Yes" "No" "Yes"
message("Age data")
## Age data
ss1b$Age
## [1] 76 71 71 76 76 79 73 65 62 69 59 69 74 81 72 70 71
message("Sex data")
## Sex data
ss1b$Sex
## [1] "M" "F" "M" "M" "F" "F" "F" "F" "M" "F" "M" "F" "F" "F" "M" "M" "M"
x1b <- axx[,colnames(axx) %in% rownames(ss1b)]
message("count matrix dimensions before filtering out low genes")
## count matrix dimensions before filtering out low genes
dim(x1b)
## [1] 60651 17
x1b <- x1b[which(rowMeans(x1b)>=10),]
message("count matrix dimensions after filtering out low genes")
## count matrix dimensions after filtering out low genes
dim(x1b)
## [1] 18412 17
x1b <- x1b[,order(colnames(x1b))]
ss1b <- ss1b[order(rownames(ss1b)),]
ss1b %>%
kbl(caption = "sample sheet") %>%
kable_paper("hover", full_width = F)
Participant_ID | Case | Redcap_ID | Tissue | fastq | pvt.pub | Age | Sex | Primary_OA | Cuff_Arthropathy | Prosthesis | Affected_Side | Height_cm | Weight_kg | BMI | ASA | Smoking | Diabetes | Hypercholesterolaemia | Hypertension | Thyroid | CRP | Creat | eGFR | Urea | Fast_Glucose | hba1c | Metabolic_Syndrome | Tendon_integrity_2_years_post.op | ASES_2_years_post.op_Pain | ASES_2_years_post.op_ADL | ASES_2_years_post.op_Total | Oxford_Baseline | Oxford_3_month | Oxford_12_month | Oxford_24_month | QuickDASH_ | QuickDASH_3_month | QuickDASH_12_month | QuickDASH_24_month | EQ.5D.3L_Baseline | EQ.5D.3L_3_month | EQ.5D.3L_12_month | EQ.5D.3L_24_month | EQVAS_Baseline | EQVAS_3_month | EQVAS_12_month | EQVAS_24_month | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
11B_S22 | AD-CAB_4011 | OA | 87 | bone | 11B_S22_L001_R1_001.fastq.gz | pub | 76 | M | Yes | No | Reverse | Right | 180 | 92 | 28 | 2 | Never_smoker | No | Yes | Yes | No | 4.0 | 75 | 85 | 7.0 | 6.0 | 6.0 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
12B_S23 | AD-CAB_4012 | OA | 91 | bone | 12B_S23_L001_R1_001.fastq.gz | pub | 71 | F | Yes | No | Anatomic | Right | 163 | 83 | 31 | 2 | Never_smoker | No | Yes | Yes | No | 2.9 | 73 | 72 | 4.8 | 6.3 | 5.7 | Yes | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
14B_S25 | AD-CAB_4014 | OA | 92 | bone | 14B_S25_L001_R1_001.fastq.gz | pvt | 71 | M | Yes | No | Reverse | Right | 170 | 99 | 34 | 2 | Ever_smoker | No | Yes | No | Yes | 2.9 | 69 | 90 | 7.0 | 7.0 | 7.1 | Yes | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
15B_S26 | AD-CAB_4015 | OA | 93 | bone | 15B_S26_L001_R1_001.fastq.gz | pvt | 76 | M | Yes | No | Anatomic | Left | 183 | 95 | 28 | 2 | Ever_smoker | No | Yes | Yes | No | 5.6 | 90 | 71 | 6.6 | 5.5 | 5.0 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
16B_S27 | AD-CAB_4016 | OA | 99 | bone | 16B_S27_L001_R1_001.fastq.gz | pvt | 76 | F | Yes | No | Anatomic | Left | 167 | 54 | 19 | 3 | Ever_smoker | No | No | No | Yes | 2.9 | 60 | 86 | 11.0 | 4.7 | 5.3 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
17B_S28 | AD-CAB_4017 | OA | 96 | bone | 17B_S28_L001_R1_001.fastq.gz | pvt | 79 | F | Yes | No | Reverse | Right | 155 | 75 | 31 | 2 | Never_smoker | No | No | No | No | 9.2 | 71 | 70 | 4.5 | 5.5 | 5.1 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
18B_S29 | AD-CAB_4018 | OA | 97 | bone | 18B_S29_L001_R1_001.fastq.gz | pvt | 73 | F | Yes | No | Anatomic | Right | 167 | 85 | 30 | 3 | Ever_smoker | No | Yes | No | No | 1.5 | 78 | 65 | 7.3 | 5.4 | 5.9 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
19B_S30 | AD-CAB_4019 | OA | 95 | bone | 19B_S30_L001_R1_001.fastq.gz | pvt | 65 | F | Yes | No | Anatomic | Left | 170 | 62 | 21 | 2 | Never_smoker | No | No | Yes | No | 2.9 | 103 | 49 | 11.0 | 5.3 | 5.2 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
20B_S31 | AD-CAB_4020 | OA | 98 | bone | 20B_S31_L001_R1_001.fastq.gz | pvt | 62 | M | Yes | No | Anatomic | Left | 180 | 117 | 36 | 2 | Never_smoker | No | Yes | No | No | 2.9 | 80 | 90 | 4.9 | 6.9 | 5.9 | Yes | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
4001.41B | AD-CAB_4001 | OA | 84 | bone | 4001-41B_R1_001.fastq.gz | pvt | 69 | F | Yes | No | Anatomic | Left | 158 | 89 | 36 | 2 | Never_smoker | No | Yes | Yes | Yes | 2.9 | 66 | 82 | 5.2 | 5.7 | 6.1 | Yes | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
4002.42B | AD-CAB_4002 | OA | 80 | bone | 4002-42B_R1_001.fastq.gz | pvt | 59 | M | Yes | No | Anatomic | Left | 182 | 106 | 32 | 1 | Ever_smoker | No | Yes | No | No | 9.3 | 69 | 90 | 4.3 | 6.2 | 5.4 | Yes | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
4004.44B | AD-CAB_4004 | OA | 82 | bone | 4004-44B_R1_001.fastq.gz | pvt | 69 | F | Yes | No | Anatomic | Left | 165 | 85 | 32 | 2 | Never_smoker | No | Yes | Yes | Yes | 3.9 | 61 | 89 | 5.8 | 5.8 | 5.6 | Yes | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
4005.45B | AD-CAB_4005 | OA | 83 | bone | 4005-45B_R1_001.fastq.gz | pvt | 74 | F | Yes | No | Anatomic | Left | 169 | 75 | 26 | 2 | Ever_smoker | No | Yes | Yes | No | 2.9 | 90 | 72 | 6.6 | 5.2 | 5.7 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
4006.46B | AD-CAB_4006 | OA | 78 | bone | 4006-46B_R1_001.fastq.gz | pvt | 81 | F | Yes | No | Anatomic | Right | 150 | 54 | 24 | 3 | Never_smoker | No | Yes | Yes | No | 2.9 | 105 | 43 | 10.5 | 5.6 | 6.0 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
7B_S18 | AD-CAB_4007 | OA | 85 | bone | 7B_S18_L001_R1_001.fastq.gz | pvt | 72 | M | Yes | No | Anatomic | Right | 184 | 118 | 35 | 2 | Ever_smoker | No | Yes | Yes | No | 12.7 | 66 | 90 | 5.8 | 5.6 | 5.6 | Yes | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
8B_S19 | AD-CAB_4008 | OA | 86 | bone | 8B_S19_L001_R1_001.fastq.gz | pub | 70 | M | Yes | No | Anatomic | Right | 172 | 86 | 29 | 2 | Never_smoker | No | No | Yes | No | 2.9 | 103 | 64 | 7.9 | 5.6 | 5.6 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
SL2.08Re_S60 | AD-CAB_4014 | OA | 92 | bone | SL2-08Re_S60_L001_R1_001.fastq.gz | pvt | 71 | M | Yes | No | Reverse | Right | 170 | 99 | 34 | 2 | Ever_smoker | No | Yes | No | Yes | 2.9 | 69 | 90 | 7.0 | 7.0 | 7.1 | Yes | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
plotMDS(x1b)
message("here is the model spec:")
## here is the model spec:
dds <- DESeqDataSetFromMatrix(countData = x1b , colData = ss1b, design = ~ Metabolic_Syndrome )
## converting counts to integer mode
## Warning in DESeqDataSet(se, design = design, ignoreRank): some variables in
## design formula are characters, converting to factors
res <- DESeq(dds)
## estimating size factors
## estimating dispersions
## gene-wise dispersion estimates
## mean-dispersion relationship
## final dispersion estimates
## fitting model and testing
## -- replacing outliers and refitting for 220 genes
## -- DESeq argument 'minReplicatesForReplace' = 7
## -- original counts are preserved in counts(dds)
## estimating dispersions
## fitting model and testing
z<- results(res)
vsd <- vst(dds, blind=FALSE)
zz <- cbind(as.data.frame(z),assay(vsd))
dge <- as.data.frame(zz[order(zz$pvalue),])
dge[1:20,1:6] %>%
kbl(caption = "Top DEGs in bone between OA patients with and without metabolic syndrome.") %>%
kable_paper("hover", full_width = F)
baseMean | log2FoldChange | lfcSE | stat | pvalue | padj | |
---|---|---|---|---|---|---|
ENSG00000185269.12.NOTUM | 21.84588 | 4.9570549 | 0.6003943 | 8.256332 | 0 | 0.00e+00 |
ENSG00000182600.9.SNORC | 80.88169 | 4.4220506 | 0.6359907 | 6.953011 | 0 | 0.00e+00 |
ENSG00000167123.19.CERCAM | 872.63471 | 2.2353965 | 0.3375271 | 6.622864 | 0 | 2.00e-07 |
ENSG00000138028.16.CGREF1 | 171.46614 | 2.5876088 | 0.3921460 | 6.598585 | 0 | 2.00e-07 |
ENSG00000142552.8.RCN3 | 954.08139 | 1.6072791 | 0.2467885 | 6.512779 | 0 | 3.00e-07 |
ENSG00000184471.8.C1QTNF8 | 27.80265 | 3.6632986 | 0.5911882 | 6.196501 | 0 | 1.70e-06 |
ENSG00000130600.19.H19 | 2387.16438 | 2.7108388 | 0.4584606 | 5.912915 | 0 | 8.30e-06 |
ENSG00000111199.12.TRPV4 | 163.35305 | 2.7838090 | 0.4741709 | 5.870898 | 0 | 9.40e-06 |
ENSG00000183010.17.PYCR1 | 297.80178 | 1.6239497 | 0.2790084 | 5.820433 | 0 | 1.13e-05 |
ENSG00000106415.13.GLCCI1 | 203.22265 | -0.9088876 | 0.1570326 | -5.787891 | 0 | 1.18e-05 |
ENSG00000139219.19.COL2A1 | 3398.50699 | 4.9972080 | 0.8647172 | 5.779008 | 0 | 1.18e-05 |
ENSG00000138316.11.ADAMTS14 | 115.57690 | 2.1902355 | 0.3820337 | 5.733094 | 0 | 1.42e-05 |
ENSG00000113739.11.STC2 | 44.58732 | 3.1362855 | 0.5483919 | 5.719058 | 0 | 1.43e-05 |
ENSG00000136457.10.CHAD | 3017.47160 | 2.9434500 | 0.5195108 | 5.665811 | 0 | 1.77e-05 |
ENSG00000157766.19.ACAN | 819.95444 | 3.4146378 | 0.6034953 | 5.658102 | 0 | 1.77e-05 |
ENSG00000137441.8.FGFBP2 | 596.89753 | 3.6004791 | 0.6416477 | 5.611302 | 0 | 2.18e-05 |
ENSG00000183196.10.CHST6 | 92.17133 | 3.0945377 | 0.5555569 | 5.570154 | 0 | 2.60e-05 |
ENSG00000204248.11.COL11A2 | 345.76660 | 1.8920244 | 0.3442054 | 5.496788 | 0 | 3.73e-05 |
ENSG00000281990.1.IGHV1.69.2 | 19.94618 | -6.2076100 | 1.1364487 | -5.462288 | 0 | 4.11e-05 |
ENSG00000141756.19.FKBP10 | 1435.20660 | 2.1650418 | 0.3970311 | 5.453079 | 0 | 4.11e-05 |
message("here is the model spec:")
## here is the model spec:
dds <- DESeqDataSetFromMatrix(countData = x1b , colData = ss1b, design = ~ Age + Sex + CRP + Metabolic_Syndrome )
## converting counts to integer mode
## Warning in DESeqDataSet(se, design = design, ignoreRank): some variables in
## design formula are characters, converting to factors
## the design formula contains one or more numeric variables with integer values,
## specifying a model with increasing fold change for higher values.
## did you mean for this to be a factor? if so, first convert
## this variable to a factor using the factor() function
## the design formula contains one or more numeric variables that have mean or
## standard deviation larger than 5 (an arbitrary threshold to trigger this message).
## Including numeric variables with large mean can induce collinearity with the intercept.
## Users should center and scale numeric variables in the design to improve GLM convergence.
res <- DESeq(dds)
## estimating size factors
## estimating dispersions
## gene-wise dispersion estimates
## mean-dispersion relationship
## final dispersion estimates
## fitting model and testing
## 1 rows did not converge in beta, labelled in mcols(object)$betaConv. Use larger maxit argument with nbinomWaldTest
z<- results(res)
vsd <- vst(dds, blind=FALSE)
zz <- cbind(as.data.frame(z),assay(vsd))
dge <- as.data.frame(zz[order(zz$pvalue),])
dge[1:20,1:6] %>%
kbl(caption = "Top DEGs in bone between OA patients with and without metabolic syndrome, adjusted for age, sex and CRP.") %>%
kable_paper("hover", full_width = F)
baseMean | log2FoldChange | lfcSE | stat | pvalue | padj | |
---|---|---|---|---|---|---|
ENSG00000182600.9.SNORC | 80.88169 | 4.230058 | 0.6478397 | 6.529482 | 0.0e+00 | 0.0000012 |
ENSG00000164106.8.SCRG1 | 226.95372 | 3.418468 | 0.5460676 | 6.260156 | 0.0e+00 | 0.0000034 |
ENSG00000186205.13.MTARC1 | 317.46675 | -1.235527 | 0.2028667 | -6.090336 | 0.0e+00 | 0.0000066 |
ENSG00000185269.12.NOTUM | 21.84588 | 4.631073 | 0.8011530 | 5.780510 | 0.0e+00 | 0.0000330 |
ENSG00000171724.3.VAT1L | 23.44098 | 2.034787 | 0.3672296 | 5.540913 | 0.0e+00 | 0.0001065 |
ENSG00000120885.22.CLU | 12652.00431 | 3.397077 | 0.6201745 | 5.477614 | 0.0e+00 | 0.0001272 |
ENSG00000157766.19.ACAN | 1526.34053 | 4.245406 | 0.7803311 | 5.440518 | 1.0e-07 | 0.0001343 |
ENSG00000113739.11.STC2 | 44.58732 | 3.653243 | 0.6766547 | 5.398977 | 1.0e-07 | 0.0001470 |
ENSG00000198892.7.SHISA4 | 70.95831 | 2.167296 | 0.4028927 | 5.379338 | 1.0e-07 | 0.0001470 |
ENSG00000176971.4.FIBIN | 147.94606 | 3.109228 | 0.5850656 | 5.314325 | 1.0e-07 | 0.0001846 |
ENSG00000177106.16.EPS8L2 | 130.25154 | 2.131447 | 0.4020334 | 5.301666 | 1.0e-07 | 0.0001846 |
ENSG00000137441.8.FGFBP2 | 596.89753 | 3.549677 | 0.6814745 | 5.208818 | 2.0e-07 | 0.0002803 |
ENSG00000102313.9.ITIH6 | 38.89310 | 5.202700 | 1.0050249 | 5.176688 | 2.0e-07 | 0.0003075 |
ENSG00000130600.19.H19 | 2387.16438 | 3.035993 | 0.5916549 | 5.131358 | 3.0e-07 | 0.0003636 |
ENSG00000261857.7.MIA | 115.03440 | 3.796352 | 0.7423445 | 5.114003 | 3.0e-07 | 0.0003721 |
ENSG00000154143.3.PANX3 | 13.86380 | 4.118535 | 0.8083235 | 5.095157 | 3.0e-07 | 0.0003854 |
ENSG00000260428.3.SCX | 38.97017 | 1.833260 | 0.3620788 | 5.063153 | 4.0e-07 | 0.0004293 |
ENSG00000111199.12.TRPV4 | 163.35305 | 2.907016 | 0.5843122 | 4.975108 | 7.0e-07 | 0.0006412 |
ENSG00000237172.4.B3GNT9 | 151.84508 | 1.733289 | 0.3547988 | 4.885272 | 1.0e-06 | 0.0009621 |
ENSG00000188338.15.SLC38A3 | 26.63005 | 3.328527 | 0.6874607 | 4.841771 | 1.3e-06 | 0.0010543 |
dge1b <- dge
Now run a mitch analysis.
gnames <- sapply(strsplit(sub("\\."," ",sub("\\."," ",rownames(axx))) ," "),"[[",3)
gt <- data.frame(rownames(axx),gnames)
gs <- gmt_import("ReactomePathways_2023-09-01.gmt")
dge1b$gn <- sapply(strsplit( sub("\\.","_", ( sub("\\.","_",rownames(dge1b)) ) ), "_"),"[[",3)
m <- mitch_import(x=dge1b,DEtype="DESeq2",geneTable=gt)
## The input is a single dataframe; one contrast only. Converting
## it to a list for you.
## Note: Mean no. genes in input = 18412
## Note: no. genes in output = 18383
## Note: estimated proportion of input genes in output = 0.998
mres1b <- mitch_calc(x=m,genesets=gs,cores=16,priority="effect")
## Note: Enrichments with large effect sizes may not be
## statistically significant.
head(mres1b$enrichment_result,20) %>%
kbl(caption = "Top Reactomes for dge1b") %>%
kable_paper("hover", full_width = F)
set | setSize | pANOVA | s.dist | p.adjustANOVA | |
---|---|---|---|---|---|
1435 | Unwinding of DNA | 12 | 0.0000113 | -0.7317965 | 0.0000835 |
535 | Heme biosynthesis | 13 | 0.0000060 | -0.7246849 | 0.0000483 |
897 | Polo-like kinase mediated events | 16 | 0.0000006 | -0.7194493 | 0.0000068 |
53 | Activation of the pre-replicative complex | 32 | 0.0000000 | -0.7162280 | 0.0000000 |
375 | Establishment of Sister Chromatid Cohesion | 11 | 0.0000418 | -0.7133484 | 0.0002650 |
450 | G0 and Early G1 | 27 | 0.0000000 | -0.6985142 | 0.0000000 |
373 | Erythropoietin activates Phosphoinositide-3-kinase (PI3K) | 11 | 0.0000680 | -0.6935059 | 0.0004117 |
236 | Crosslinking of collagen fibrils | 17 | 0.0000010 | 0.6851023 | 0.0000101 |
1376 | Transcription of E2F targets under negative control by DREAM complex | 19 | 0.0000003 | -0.6817286 | 0.0000033 |
211 | Collagen biosynthesis and modifying enzymes | 63 | 0.0000000 | 0.6810737 | 0.0000000 |
734 | Mitotic Telophase/Cytokinesis | 13 | 0.0000233 | -0.6774926 | 0.0001559 |
310 | Diseases associated with glycosaminoglycan metabolism | 36 | 0.0000000 | 0.6670694 | 0.0000000 |
1377 | Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 | 16 | 0.0000046 | -0.6615601 | 0.0000378 |
454 | G1/S-Specific Transcription | 29 | 0.0000000 | -0.6537183 | 0.0000000 |
219 | Condensation of Prometaphase Chromosomes | 11 | 0.0001741 | -0.6535934 | 0.0009609 |
264 | DNA strand elongation | 32 | 0.0000000 | -0.6479654 | 0.0000000 |
670 | MET activates PTK2 signaling | 29 | 0.0000000 | 0.6458087 | 0.0000000 |
220 | Condensation of Prophase Chromosomes | 24 | 0.0000001 | -0.6407166 | 0.0000008 |
36 | Activation of ATR in response to replication stress | 37 | 0.0000000 | -0.6372256 | 0.0000000 |
145 | CS/DS degradation | 11 | 0.0002570 | 0.6364032 | 0.0013586 |
mitch_report(res=mres1b,outfile="mitch1boa_report.html",overwrite=TRUE)
## Note: overwriting existing report
## Dataset saved as " /tmp/RtmpQCsbbz/mitch1boa_report.rds ".
##
##
## processing file: mitch.Rmd
## 1/34
## 2/34 [checklibraries]
## 3/34
## 4/34 [peek]
## 5/34
## 6/34 [metrics]
## 7/34
## 8/34 [scatterplot]
## 9/34
## 10/34 [contourplot]
## 11/34
## 12/34 [input_geneset_metrics1]
## 13/34
## 14/34 [input_geneset_metrics2]
## 15/34
## 16/34 [input_geneset_metrics3]
## 17/34
## 18/34 [echart1d]
## 19/34 [echart2d]
## 20/34
## 21/34 [heatmap]
## 22/34
## 23/34 [effectsize]
## 24/34
## 25/34 [results_table]
## 26/34
## 27/34 [results_table_complete]
## 28/34
## 29/34 [detailed_geneset_reports1d]
## 30/34
## 31/34 [detailed_geneset_reports2d]
## 32/34
## 33/34 [session_info]
## 34/34
## output file: /mnt/data/mdz/projects/shoulder/shoulder-instability-osteroarthritis/mitch.knit.md
## /home/mdz/anaconda3/bin/pandoc +RTS -K512m -RTS /mnt/data/mdz/projects/shoulder/shoulder-instability-osteroarthritis/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpQCsbbz/mitch_report.html --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpQCsbbz/rmarkdown-str38ec93250a3b6e.html
##
## Output created: /tmp/RtmpQCsbbz/mitch_report.html
## [1] TRUE
Need to:
select cuff arthropathy samples only
look at the effect of metabolic syndrome in OA (ss1).
consider tissues as “batches” to correct for.
Unfortunately it isn’t possible to correct for participant “batches” at the same time.
ss1 <- subset(ss,Cuff_Arthropathy=="Yes")
message("Metabolic syndrome classification")
## Metabolic syndrome classification
ss1$Metabolic_Syndrome
## [1] "No" "No" "No" "No" "Yes" "Yes" "Yes" "Yes" "No" "Yes" "Yes" "Yes"
## [13] "No" "No" "No"
message("Age data")
## Age data
ss1$Age
## [1] 80 80 80 76 69 69 69 71 79 74 74 74 72 72 72
message("Sex data")
## Sex data
ss1$Sex
## [1] "F" "F" "F" "M" "F" "F" "F" "M" "F" "F" "F" "F" "M" "M" "M"
x1 <- axx[,colnames(axx) %in% rownames(ss1)]
message("count matrix dimensions before filtering out low genes")
## count matrix dimensions before filtering out low genes
dim(x1)
## [1] 60651 15
x1 <- x1[which(rowMeans(x1)>=10),]
message("count matrix dimensions after filtering out low genes")
## count matrix dimensions after filtering out low genes
dim(x1)
## [1] 17836 15
x1 <- x1[,order(colnames(x1))]
ss1 <- ss1[order(rownames(ss1)),]
ss1 %>%
kbl(caption = "sample sheet") %>%
kable_paper("hover", full_width = F)
Participant_ID | Case | Redcap_ID | Tissue | fastq | pvt.pub | Age | Sex | Primary_OA | Cuff_Arthropathy | Prosthesis | Affected_Side | Height_cm | Weight_kg | BMI | ASA | Smoking | Diabetes | Hypercholesterolaemia | Hypertension | Thyroid | CRP | Creat | eGFR | Urea | Fast_Glucose | hba1c | Metabolic_Syndrome | Tendon_integrity_2_years_post.op | ASES_2_years_post.op_Pain | ASES_2_years_post.op_ADL | ASES_2_years_post.op_Total | Oxford_Baseline | Oxford_3_month | Oxford_12_month | Oxford_24_month | QuickDASH_ | QuickDASH_3_month | QuickDASH_12_month | QuickDASH_24_month | EQ.5D.3L_Baseline | EQ.5D.3L_3_month | EQ.5D.3L_12_month | EQ.5D.3L_24_month | EQVAS_Baseline | EQVAS_3_month | EQVAS_12_month | EQVAS_24_month | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
10B_S21 | AD-CAB_4010 | OA | 90 | bone | 10B_S21_L001_R1_001.fastq.gz | pvt | 80 | F | No | Yes | Reverse | Left | 161 | 72 | 28 | 2 | Never_smoker | No | Yes | No | Yes | 11.2 | 54 | 86 | 8.5 | 7.3 | 5.6 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
10C_S35 | AD-CAB_4010 | OA | 90 | capsule | 10C_S35_L001_R1_001.fastq.gz | pvt | 80 | F | No | Yes | Reverse | Left | 161 | 72 | 28 | 2 | Never_smoker | No | Yes | No | Yes | 11.2 | 54 | 86 | 8.5 | 7.3 | 5.6 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
10S_S49 | AD-CAB_4010 | OA | 90 | synovium | 10S_S49_L001_R1_001.fastq.gz | pvt | 80 | F | No | Yes | Reverse | Left | 161 | 72 | 28 | 2 | Never_smoker | No | Yes | No | Yes | 11.2 | 54 | 86 | 8.5 | 7.3 | 5.6 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
11C_S36 | AD-CAB_4011 | OA | 87 | capsule | 11C_S36_L001_R1_001.fastq.gz | pub | 76 | M | No | Yes | Reverse | Right | 180 | 92 | 28 | 2 | Never_smoker | No | Yes | Yes | No | 4.0 | 75 | 85 | 7.0 | 6.0 | 6.0 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
13B_S24 | AD-CAB_4013 | OA | 89 | bone | 13B_S24_L001_R1_001.fastq.gz | pvt | 69 | F | No | Yes | Reverse | Left | 170 | 89 | 31 | 2 | Never_smoker | No | Yes | Yes | No | 2.9 | 81 | 85 | 5.1 | 5.4 | 5.9 | Yes | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
13C_S38 | AD-CAB_4013 | OA | 89 | capsule | 13C_S38_L001_R1_001.fastq.gz | pvt | 69 | F | No | Yes | Reverse | Left | 170 | 89 | 31 | 2 | Never_smoker | No | Yes | Yes | No | 2.9 | 81 | 85 | 5.1 | 5.4 | 5.9 | Yes | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
13S_S52 | AD-CAB_4013 | OA | 89 | synovium | 13S_S52_L001_R1_001.fastq.gz | pvt | 69 | F | No | Yes | Reverse | Left | 170 | 89 | 31 | 2 | Never_smoker | No | Yes | Yes | No | 2.9 | 81 | 85 | 5.1 | 5.4 | 5.9 | Yes | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
14C_S39 | AD-CAB_4014 | OA | 92 | capsule | 14C_S39_L001_R1_001.fastq.gz | pvt | 71 | M | No | Yes | Reverse | Right | 170 | 99 | 34 | 2 | Ever_smoker | No | Yes | No | Yes | 2.9 | 69 | 90 | 7.0 | 7.0 | 7.1 | Yes | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
17C_S42 | AD-CAB_4017 | OA | 96 | capsule | 17C_S42_L001_R1_001.fastq.gz | pvt | 79 | F | No | Yes | Reverse | Right | 155 | 75 | 31 | 2 | Never_smoker | No | No | No | No | 9.2 | 71 | 70 | 4.5 | 5.5 | 5.1 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
4003.43B | AD-CAB_4003 | OA | 81 | bone | 4003-43B_R1_001.fastq.gz | pvt | 74 | F | No | Yes | Reverse | Right | 153 | 87 | 37 | 2 | Ever_smoker | No | Yes | Yes | No | 6.9 | 77 | 66 | 5.0 | 5.4 | 5.4 | Yes | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
4003.43C | AD-CAB_4003 | OA | 81 | capsule | 4003-43C_R1_001.fastq.gz | pvt | 74 | F | No | Yes | Reverse | Right | 153 | 87 | 37 | 2 | Ever_smoker | No | Yes | Yes | No | 6.9 | 77 | 66 | 5.0 | 5.4 | 5.4 | Yes | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
4003.43S | AD-CAB_4003 | OA | 81 | synovium | 4003-43S_R1_001.fastq.gz | pvt | 74 | F | No | Yes | Reverse | Right | 153 | 87 | 37 | 2 | Ever_smoker | No | Yes | Yes | No | 6.9 | 77 | 66 | 5.0 | 5.4 | 5.4 | Yes | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
9B_S20 | AD-CAB_4009 | OA | 88 | bone | 9B_S20_L001_R1_001.fastq.gz | pvt | 72 | M | No | Yes | Reverse | Right | 167 | 80 | 29 | 3 | Ever_smoker | No | Yes | Yes | No | 2.9 | 107 | 59 | 6.7 | 5.8 | 5.5 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
9C_S34 | AD-CAB_4009 | OA | 88 | capsule | 9C_S34_L001_R1_001.fastq.gz | pvt | 72 | M | No | Yes | Reverse | Right | 167 | 80 | 29 | 3 | Ever_smoker | No | Yes | Yes | No | 2.9 | 107 | 59 | 6.7 | 5.8 | 5.5 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
9S_S48 | AD-CAB_4009 | OA | 88 | synovium | 9S_S48_L001_R1_001.fastq.gz | pvt | 72 | M | No | Yes | Reverse | Right | 167 | 80 | 29 | 3 | Ever_smoker | No | Yes | Yes | No | 2.9 | 107 | 59 | 6.7 | 5.8 | 5.5 | No | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
plotMDS(x1)
message("here is the model spec:")
## here is the model spec:
dds <- DESeqDataSetFromMatrix(countData = x1 , colData = ss1, design = ~ Tissue + Metabolic_Syndrome )
## converting counts to integer mode
## Warning in DESeqDataSet(se, design = design, ignoreRank): some variables in
## design formula are characters, converting to factors
res <- DESeq(dds)
## estimating size factors
## estimating dispersions
## gene-wise dispersion estimates
## mean-dispersion relationship
## final dispersion estimates
## fitting model and testing
z<- results(res)
vsd <- vst(dds, blind=FALSE)
zz <- cbind(as.data.frame(z),assay(vsd))
dge <- as.data.frame(zz[order(zz$pvalue),])
dge[1:20,1:6] %>%
kbl(caption = "Top DEGs that are altered in all tissues by metabolic syndrome.") %>%
kable_paper("hover", full_width = F)
baseMean | log2FoldChange | lfcSE | stat | pvalue | padj | |
---|---|---|---|---|---|---|
ENSG00000171798.18.KNDC1 | 17.52212 | -3.274925 | 0.6181115 | -5.298276 | 0.0000001 | 0.0010439 |
ENSG00000071859.15.FAM50A | 2743.93745 | -2.711501 | 0.5119569 | -5.296346 | 0.0000001 | 0.0010439 |
ENSG00000269900.3.RMRP | 74.42722 | -7.205598 | 1.4042967 | -5.131108 | 0.0000003 | 0.0016968 |
ENSG00000153266.13.FEZF2 | 33.57803 | -3.203489 | 0.6874521 | -4.659945 | 0.0000032 | 0.0139739 |
ENSG00000156076.10.WIF1 | 272.49627 | -4.115397 | 0.8988475 | -4.578526 | 0.0000047 | 0.0165503 |
ENSG00000129988.6.LBP | 97.13172 | -2.881010 | 0.6374514 | -4.519576 | 0.0000062 | 0.0182503 |
ENSG00000162188.6.GNG3 | 20.13093 | -4.216226 | 0.9603866 | -4.390135 | 0.0000113 | 0.0246764 |
ENSG00000138135.7.CH25H | 19.94769 | -2.647419 | 0.6049496 | -4.376263 | 0.0000121 | 0.0246764 |
ENSG00000174738.13.NR1D2 | 260.86392 | 1.394920 | 0.3193857 | 4.367508 | 0.0000126 | 0.0246764 |
ENSG00000101282.9.RSPO4 | 17.54382 | -3.360214 | 0.7922278 | -4.241475 | 0.0000222 | 0.0392417 |
ENSG00000196656.7.AC004057.1 | 353.96613 | 1.831635 | 0.4522281 | 4.050245 | 0.0000512 | 0.0821972 |
ENSG00000197728.11.RPS26 | 659.66768 | 1.162675 | 0.2946911 | 3.945404 | 0.0000797 | 0.1167178 |
ENSG00000256654.4.AC005906.2 | 29.77701 | 2.300732 | 0.5858120 | 3.927423 | 0.0000859 | 0.1167178 |
ENSG00000267314.1.AC104532.1 | 7.05486 | 5.307702 | 1.3632342 | 3.893463 | 0.0000988 | 0.1247431 |
ENSG00000212864.3.RNF208 | 22.84818 | -2.221922 | 0.5771325 | -3.849934 | 0.0001181 | 0.1336789 |
ENSG00000125740.14.FOSB | 2030.19009 | -3.173144 | 0.8276443 | -3.833946 | 0.0001261 | 0.1336789 |
ENSG00000123977.10.DAW1 | 31.07425 | 2.507415 | 0.6548258 | 3.829133 | 0.0001286 | 0.1336789 |
ENSG00000196091.15.MYBPC1 | 16.46819 | 3.601125 | 0.9641224 | 3.735133 | 0.0001876 | 0.1841973 |
ENSG00000214940.8.NPIPA8 | 19.30323 | 4.324186 | 1.1630242 | 3.718053 | 0.0002008 | 0.1867315 |
ENSG00000104722.14.NEFM | 39.35629 | -2.917603 | 0.7986736 | -3.653061 | 0.0002591 | 0.2224579 |
message("here is the model spec:")
## here is the model spec:
dds <- DESeqDataSetFromMatrix(countData = x1 , colData = ss1, design = ~ Age + Sex + CRP + Metabolic_Syndrome )
## converting counts to integer mode
## Warning in DESeqDataSet(se, design = design, ignoreRank): some variables in
## design formula are characters, converting to factors
## the design formula contains one or more numeric variables with integer values,
## specifying a model with increasing fold change for higher values.
## did you mean for this to be a factor? if so, first convert
## this variable to a factor using the factor() function
## the design formula contains one or more numeric variables that have mean or
## standard deviation larger than 5 (an arbitrary threshold to trigger this message).
## Including numeric variables with large mean can induce collinearity with the intercept.
## Users should center and scale numeric variables in the design to improve GLM convergence.
res <- DESeq(dds)
## estimating size factors
## estimating dispersions
## gene-wise dispersion estimates
## mean-dispersion relationship
## -- note: fitType='parametric', but the dispersion trend was not well captured by the
## function: y = a/x + b, and a local regression fit was automatically substituted.
## specify fitType='local' or 'mean' to avoid this message next time.
## final dispersion estimates
## fitting model and testing
z<- results(res)
vsd <- vst(dds, blind=FALSE)
## -- note: fitType='parametric', but the dispersion trend was not well captured by the
## function: y = a/x + b, and a local regression fit was automatically substituted.
## specify fitType='local' or 'mean' to avoid this message next time.
zz <- cbind(as.data.frame(z),assay(vsd))
dge <- as.data.frame(zz[order(zz$pvalue),])
dge[1:20,1:6] %>%
kbl(caption = "Top DEGs in bone between cuff arthropathy patients with and without metabolic syndrome, adjusted for age, sex and CRP.") %>%
kable_paper("hover", full_width = F)
baseMean | log2FoldChange | lfcSE | stat | pvalue | padj | |
---|---|---|---|---|---|---|
ENSG00000198959.12.TGM2 | 315.86349 | -3.3507315 | 0.6414867 | -5.223384 | 0.0000002 | 0.0025472 |
ENSG00000155980.13.KIF5A | 129.07520 | -4.2775322 | 0.9604122 | -4.453851 | 0.0000084 | 0.0611450 |
ENSG00000160469.17.BRSK1 | 50.46854 | -3.3693750 | 0.7810636 | -4.313829 | 0.0000160 | 0.0775459 |
ENSG00000110536.14.PTPMT1 | 167.27421 | 1.0628621 | 0.2731142 | 3.891640 | 0.0000996 | 0.2995526 |
ENSG00000163032.12.VSNL1 | 44.06568 | -4.1565301 | 1.0705245 | -3.882704 | 0.0001033 | 0.2995526 |
ENSG00000123240.17.OPTN | 590.92539 | 1.2887951 | 0.3398298 | 3.792472 | 0.0001492 | 0.3016345 |
ENSG00000144118.14.RALB | 546.14797 | 1.3212304 | 0.3504421 | 3.770182 | 0.0001631 | 0.3016345 |
ENSG00000069020.18.MAST4 | 122.05000 | -1.9906119 | 0.5286900 | -3.765178 | 0.0001664 | 0.3016345 |
ENSG00000146021.15.KLHL3 | 100.88844 | -2.2875423 | 0.6158306 | -3.714564 | 0.0002036 | 0.3018224 |
ENSG00000123200.17.ZC3H13 | 498.60552 | -0.7312717 | 0.1971671 | -3.708893 | 0.0002082 | 0.3018224 |
ENSG00000006451.8.RALA | 186.36820 | 1.4128225 | 0.3868378 | 3.652235 | 0.0002600 | 0.3216342 |
ENSG00000168209.6.DDIT4 | 1304.45036 | -2.6283417 | 0.7224367 | -3.638162 | 0.0002746 | 0.3216342 |
ENSG00000066697.15.MSANTD3 | 137.19776 | 1.8272517 | 0.5052075 | 3.616834 | 0.0002982 | 0.3216342 |
ENSG00000262879.6.AC005670.3 | 170.63779 | -1.1064848 | 0.3068179 | -3.606324 | 0.0003106 | 0.3216342 |
ENSG00000187957.8.DNER | 45.15783 | -5.1965309 | 1.5368155 | -3.381363 | 0.0007213 | 0.6513570 |
ENSG00000167775.11.CD320 | 174.06002 | -2.4803583 | 0.7388680 | -3.356971 | 0.0007880 | 0.6513570 |
ENSG00000136997.21.MYC | 358.06883 | -1.8769850 | 0.5594960 | -3.354779 | 0.0007943 | 0.6513570 |
ENSG00000196656.7.AC004057.1 | 353.96613 | 2.9485435 | 0.8907317 | 3.310249 | 0.0009321 | 0.6513570 |
ENSG00000157601.15.MX1 | 259.68722 | 1.6875061 | 0.5120564 | 3.295547 | 0.0009823 | 0.6513570 |
ENSG00000185115.6.NSMCE3 | 98.35523 | 1.0260843 | 0.3117454 | 3.291418 | 0.0009968 | 0.6513570 |
dge1 <- dge
Now run a mitch analysis.
gnames <- sapply(strsplit(sub("\\."," ",sub("\\."," ",rownames(axx))) ," "),"[[",3)
gt <- data.frame(rownames(axx),gnames)
gs <- gmt_import("ReactomePathways_2023-09-01.gmt")
dge1$gn <- sapply(strsplit( sub("\\.","_", ( sub("\\.","_",rownames(dge1)) ) ), "_"),"[[",3)
m <- mitch_import(x=dge1,DEtype="DESeq2",geneTable=gt)
## The input is a single dataframe; one contrast only. Converting
## it to a list for you.
## Note: Mean no. genes in input = 17836
## Note: no. genes in output = 17810
## Note: estimated proportion of input genes in output = 0.999
mres1 <- mitch_calc(x=m,genesets=gs,cores=16,priority="effect")
## Note: Enrichments with large effect sizes may not be
## statistically significant.
head(mres1$enrichment_result,20) %>%
kbl(caption = "Top Reactomes for dge1b") %>%
kable_paper("hover", full_width = F)
set | setSize | pANOVA | s.dist | p.adjustANOVA | |
---|---|---|---|---|---|
413 | Folding of actin by CCT/TriC | 10 | 0.0002124 | 0.6763258 | 0.0011235 |
638 | LGI-ADAM interactions | 11 | 0.0003973 | -0.6166894 | 0.0019000 |
375 | Establishment of Sister Chromatid Cohesion | 11 | 0.0004628 | 0.6096410 | 0.0021652 |
107 | BBSome-mediated cargo-targeting to cilium | 21 | 0.0000027 | 0.5914972 | 0.0000198 |
1085 | Regulation of ornithine decarboxylase (ODC) | 48 | 0.0000000 | 0.5786229 | 0.0000000 |
1138 | SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs | 11 | 0.0009390 | 0.5760130 | 0.0040626 |
722 | Mitochondrial translation initiation | 88 | 0.0000000 | 0.5668981 | 0.0000000 |
723 | Mitochondrial translation termination | 88 | 0.0000000 | 0.5656311 | 0.0000000 |
720 | Mitochondrial translation | 94 | 0.0000000 | 0.5653863 | 0.0000000 |
210 | Cohesin Loading onto Chromatin | 10 | 0.0020277 | 0.5635730 | 0.0079255 |
248 | Cytosolic tRNA aminoacylation | 24 | 0.0000019 | 0.5618230 | 0.0000142 |
1105 | Response to metal ions | 11 | 0.0012710 | -0.5610887 | 0.0052998 |
721 | Mitochondrial translation elongation | 88 | 0.0000000 | 0.5556614 | 0.0000000 |
1446 | Vif-mediated degradation of APOBEC3G | 52 | 0.0000000 | 0.5547684 | 0.0000000 |
1071 | Regulation of activated PAK-2p34 by proteasome mediated degradation | 48 | 0.0000000 | 0.5514113 | 0.0000000 |
1454 | Vpu mediated degradation of CD4 | 50 | 0.0000000 | 0.5481734 | 0.0000000 |
470 | GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 | 52 | 0.0000000 | 0.5452515 | 0.0000000 |
414 | Formation of ATP by chemiosmotic coupling | 16 | 0.0001622 | 0.5445515 | 0.0008929 |
1139 | SLBP independent Processing of Histone Pre-mRNAs | 10 | 0.0032467 | 0.5375056 | 0.0120006 |
1034 | Regulation of Apoptosis | 51 | 0.0000000 | 0.5353320 | 0.0000000 |
mitch_report(res=mres1,outfile="mitch1_report.html",overwrite=TRUE)
## Note: overwriting existing report
## Dataset saved as " /tmp/RtmpQCsbbz/mitch1_report.rds ".
##
##
## processing file: mitch.Rmd
## 1/34
## 2/34 [checklibraries]
## 3/34
## 4/34 [peek]
## 5/34
## 6/34 [metrics]
## 7/34
## 8/34 [scatterplot]
## 9/34
## 10/34 [contourplot]
## 11/34
## 12/34 [input_geneset_metrics1]
## 13/34
## 14/34 [input_geneset_metrics2]
## 15/34
## 16/34 [input_geneset_metrics3]
## 17/34
## 18/34 [echart1d]
## 19/34 [echart2d]
## 20/34
## 21/34 [heatmap]
## 22/34
## 23/34 [effectsize]
## 24/34
## 25/34 [results_table]
## 26/34
## 27/34 [results_table_complete]
## 28/34
## 29/34 [detailed_geneset_reports1d]
## 30/34
## 31/34 [detailed_geneset_reports2d]
## 32/34
## 33/34 [session_info]
## 34/34
## output file: /mnt/data/mdz/projects/shoulder/shoulder-instability-osteroarthritis/mitch.knit.md
## /home/mdz/anaconda3/bin/pandoc +RTS -K512m -RTS /mnt/data/mdz/projects/shoulder/shoulder-instability-osteroarthritis/mitch.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/RtmpQCsbbz/mitch_report.html --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /usr/local/lib/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --section-divs --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpQCsbbz/rmarkdown-str38ec936a02d103.html
##
## Output created: /tmp/RtmpQCsbbz/mitch_report.html
## [1] TRUE
Need to:
Select rotator cuff
look at the effect of metabolic syndrome.
ss2 <- subset(ss,Case=="RC")
ss2c <- subset(ss2,Tissue=="capsule")
message("Metabolic syndrome classification")
## Metabolic syndrome classification
ss2c$Metabolic_Syndrome
## [1] "Yes" "No" "No" "No" "Yes" "Yes" "Yes" "No" "No" "No" "Yes" "No"
## [13] "No" "No" NA "No" "No" "Yes" "Yes" "No" "No" NA "No" "No"
## [25] "No" "No"
message("Age data")
## Age data
ss2c$Age
## [1] 67 58 50 72 68 70 66 68 60 72 45 58 61 46 39 58 52 62 59 56 68 59 65 63 70
## [26] 68
message("Sex data")
## Sex data
ss2c$Sex
## [1] "M" "M" "M" "M" "F" "M" "M" "M" "M" "M" "F" "M" "M" "M" "F" "M" "F" "F" "M"
## [20] "M" "M" "F" "M" "F" "M" "M"
x2c <- axx[,colnames(axx) %in% rownames(ss2c)]
message("count matrix dimensions before filtering out low genes")
## count matrix dimensions before filtering out low genes
dim(x2c)
## [1] 60651 26
x2c <- x2c[which(rowMeans(x2c)>=10),]
message("count matrix dimensions after filtering out low genes")
## count matrix dimensions after filtering out low genes
dim(x2c)
## [1] 16169 26
x2c <- x2c[,order(colnames(x2c))]
ss2c <- ss2c[order(rownames(ss2c)),]
ss2c <- subset(ss2c,Metabolic_Syndrome=="No" | Metabolic_Syndrome=="Yes")
x2c <- x2c[,colnames(x2c) %in% rownames(ss2c)]
ss2c %>%
kbl(caption = "sample sheet") %>%
kable_paper("hover", full_width = F)
Participant_ID | Case | Redcap_ID | Tissue | fastq | pvt.pub | Age | Sex | Primary_OA | Cuff_Arthropathy | Prosthesis | Affected_Side | Height_cm | Weight_kg | BMI | ASA | Smoking | Diabetes | Hypercholesterolaemia | Hypertension | Thyroid | CRP | Creat | eGFR | Urea | Fast_Glucose | hba1c | Metabolic_Syndrome | Tendon_integrity_2_years_post.op | ASES_2_years_post.op_Pain | ASES_2_years_post.op_ADL | ASES_2_years_post.op_Total | Oxford_Baseline | Oxford_3_month | Oxford_12_month | Oxford_24_month | QuickDASH_ | QuickDASH_3_month | QuickDASH_12_month | QuickDASH_24_month | EQ.5D.3L_Baseline | EQ.5D.3L_3_month | EQ.5D.3L_12_month | EQ.5D.3L_24_month | EQVAS_Baseline | EQVAS_3_month | EQVAS_12_month | EQVAS_24_month | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1.1_S41 | AD-CAB_3001 | RC | 53 | capsule | 1-1_S41_L001_R1_001.fastq.gz | NA | 67 | M | NA | NA | NA | Left | 177.80 | 120 | 37.90 | 2 | Ever_smoker | No | Yes | Yes | No | 2.9 | 83 | 84 | 7.0 | 5.2 | 5.6 | Yes | Torn | NA | NA | NA | 25 | 41 | 46 | NA | 38.6 | 13.6 | 13.6 | NA | 11222 | 11123 | 21222 | NA | 90 | 50 | 60 | NA |
10.1_S50 | AD-CAB_3010 | RC | 62 | capsule | 10-1_S50_L001_R1_001.fastq.gz | NA | 58 | M | NA | NA | NA | Left | 179.00 | 98 | 30.00 | 2 | Never_smoker | No | No | No | Yes | 2.9 | 82 | 90 | 5.6 | 4.9 | 5.1 | No | Intact | 45 | 17 | 62 | 21 | 45 | 43 | 44 | 45.5 | 4.5 | 11.4 | 20.5 | 11221 | 11111 | 11121 | 11221 | 70 | 70 | 75 | 85 |
11.1_S51 | AD-CAB_3011 | RC | 63 | capsule | 11-1_S51_L001_R1_001.fastq.gz | NA | 50 | M | NA | NA | NA | Right | 180.00 | 82 | 25.00 | 1 | Never_smoker | No | Yes | No | No | 2.9 | 99 | 76 | 6.7 | 5.7 | 6.0 | No | Intact | 35 | 18 | 53 | 18 | 38 | 44 | 46 | 61.4 | 31.8 | 6.8 | 20.5 | 11221 | 11222 | 11111 | 11121 | 75 | 83 | 75 | 78 |
12.1_S52 | AD-CAB_3012 | RC | 64 | capsule | 12-1_S52_L001_R1_001.fastq.gz | NA | 72 | M | NA | NA | NA | Left | 173.00 | 87 | 29.00 | 3 | Never_smoker | Yes | Yes | Yes | No | 2.9 | 108 | 59 | 4.8 | 6.1 | 6.6 | No | NA | 50 | 48 | 98 | 29 | 32 | 48 | 42 | 68.2 | 0.0 | 4.5 | 18.2 | 12221 | 11111 | 11111 | 11111 | 70 | 90 | 80 | 90 |
13.1_S53 | AD-CAB_3013 | RC | 65 | capsule | 13-1_S53_L001_R1_001.fastq.gz | NA | 68 | F | NA | NA | NA | Right | 161.00 | 104 | 40.00 | 3 | Never_smoker | Yes | No | Yes | No | 6.3 | 64 | 86 | 6.8 | 9.2 | 7.1 | Yes | NA | 45 | 45 | 90 | 19 | 34 | 48 | 46 | 75.0 | 50.0 | 6.8 | 2.3 | 11222 | 11221 | 22221 | 21231 | 89 | 78 | 50 | 50 |
14.1_S54 | AD-CAB_3014 | RC | 66 | capsule | 14-1_S54_L001_R1_001.fastq.gz | NA | 70 | M | NA | NA | NA | Left | 1.77 | 100 | 32.00 | 3 | Ever_smoker | No | Yes | Yes | No | 2.9 | 86 | 79 | 7.1 | 6.3 | 5.8 | Yes | Intact | 50 | 45 | 95 | 27 | 43 | 47 | 47 | 50.0 | 9.1 | 6.8 | 9.1 | 12221 | 11111 | 11111 | 11111 | 90 | 90 | 88 | 85 |
15.1_S55 | AD-CAB_3015 | RC | 69 | capsule | 15-1_S55_L001_R1_001.fastq.gz | NA | 66 | M | NA | NA | NA | Left | 175.00 | 95 | 31.00 | 3 | Never_smoker | No | Yes | Yes | No | 2.9 | 53 | 90 | 4.1 | 5.5 | 5.2 | Yes | Intact | 50 | 47 | 97 | 25 | NA | NA | 48 | 40.9 | NA | NA | 13.6 | 11121 | NA | NA | 11121 | 78 | NA | NA | 93 |
16.1_S56 | AD-CAB_3016 | RC | 71 | capsule | 16-1_S56_L001_R1_001.fastq.gz | NA | 68 | M | NA | NA | NA | Left | 180.00 | 88 | 27.00 | 1 | Ever_smoker | Yes | No | Yes | No | 2.9 | 73 | 90 | 4.7 | 7.3 | 8.3 | No | Torn | 40 | 42 | 82 | 24 | 27 | 45 | 43 | 43.2 | 38.6 | 6.8 | 11.4 | 11122 | 11222 | 11112 | 11121 | 70 | 60 | 50 | 80 |
17.1_S57 | AD-CAB_3017 | RC | 70 | capsule | 17-1_S57_L001_R1_001.fastq.gz | NA | 60 | M | NA | NA | NA | Left | 166.00 | 80 | 29.00 | 2 | Ever_smoker | No | No | No | No | 2.9 | 119 | 57 | 7.2 | NA | 5.7 | No | Torn | NA | NA | NA | 13 | 40 | NA | NA | 93.2 | 38.6 | NA | NA | 12221 | 21211 | NA | NA | 70 | 60 | NA | NA |
18.1_S58 | AD-CAB_3018 | RC | 72 | capsule | 18-1_S58_L001_R1_001.fastq.gz | NA | 72 | M | NA | NA | NA | Right | 170.00 | 85 | 29.00 | 2 | Ever_smoker | No | Yes | Yes | No | 3.2 | 82 | 82 | 6.4 | 5.5 | 5.5 | No | Intact | 50 | 50 | 100 | 36 | 37 | 48 | 48 | 31.8 | 13.6 | 9.1 | 0.0 | 11122 | 11112 | 11111 | 11111 | 90 | 82 | 92 | 90 |
19.1_S59 | AD-CAB_3019 | RC | 73 | capsule | 19-1_S59_L001_R1_001.fastq.gz | NA | 45 | F | NA | NA | NA | Right | 163.00 | 98 | 36.90 | 2 | Never_smoker | No | Yes | Yes | No | 4.3 | 70 | 57 | 4.6 | 4.7 | 5.7 | Yes | Intact | 50 | 35 | 85 | 32 | 28 | 45 | 47 | 36.4 | 38.6 | 18.2 | 13.6 | 11221 | 11221 | 11121 | 11121 | 50 | 58 | 45 | 34 |
2.1_S42 | AD-CAB_3002 | RC | 54 | capsule | 2-1_S42_L001_R1_001.fastq.gz | NA | 58 | M | NA | NA | NA | Right | 179.00 | 79 | 25.00 | 1 | Never_smoker | No | No | No | No | 0.7 | 70 | 90 | 6.9 | 5.4 | 5.3 | No | Torn | NA | NA | NA | 33 | NA | 48 | NA | 29.5 | NA | 0.0 | NA | 11111 | NA | 11111 | NA | 90 | NA | 90 | NA |
20.1_S60 | AD-CAB_3020 | RC | 67 | capsule | 20-1_S60_L001_R1_001.fastq.gz | NA | 61 | M | NA | NA | NA | Right | 180.00 | 92 | 29.00 | 1 | Ever_smoker | No | No | No | No | 2.9 | 78 | 57 | 3.9 | 5.5 | 5.6 | No | Intact | 50 | 40 | 90 | 30 | 34 | 36 | 44 | 50.0 | 34.1 | 31.8 | 0.0 | 12321 | 12321 | 12211 | 12211 | 77 | 40 | 70 | 70 |
21.1_S61 | AD-CAB_3021 | RC | 68 | capsule | 21-1_S61_L001_R1_001.fastq.gz | NA | 46 | M | NA | NA | NA | Right | 180.00 | 88 | 27.20 | 2 | Never_smoker | No | Yes | No | No | 2.9 | 77 | 57 | 5.9 | 5.9 | 5.3 | No | Torn | NA | NA | NA | 29 | 44 | 43 | NA | 45.5 | 20.5 | 11.4 | NA | NA | 11111 | 11121 | NA | NA | 80 | 65 | NA |
23.1_S63 | AD-CAB_3023 | RC | 75 | capsule | 23-1_S63_L001_R1_001.fastq.gz | NA | 58 | M | NA | NA | NA | Right | 179.00 | 81 | 25.00 | 2 | Ever_smoker | No | Yes | No | No | 2.9 | 75 | 57 | 5.7 | 5.4 | 5.7 | No | Intact | 50 | 40 | 90 | 42 | 43 | 48 | 48 | 15.9 | 15.9 | 0.0 | 2.3 | 11211 | 11121 | 11111 | 11111 | 85 | 85 | 90 | 85 |
24.1_S64 | AD-CAB_3024 | RC | 76 | capsule | 24-1_S64_L001_R1_001.fastq.gz | NA | 52 | F | NA | NA | NA | Right | 153.00 | 70 | 28.00 | 2 | Never_smoker | No | Yes | Yes | Yes | 3.0 | 64 | 57 | 7.8 | 5.6 | 6.4 | No | NA | NA | NA | NA | 26 | 23 | NA | NA | 56.8 | 45.5 | NA | NA | 12222 | 12221 | NA | NA | 30 | 60 | NA | NA |
25.1_S65 | AD-CAB_3025 | RC | 77 | capsule | 25-1_S65_L001_R1_001.fastq.gz | NA | 62 | F | NA | NA | NA | Left | 157.00 | 95 | 38.50 | 2 | Never_smoker | No | Yes | Yes | No | 12.0 | 72 | 57 | 6.6 | 6.2 | 5.7 | Yes | Intact | 45 | 43 | 88 | 26 | 36 | 38 | 41 | 59.1 | 29.5 | 31.8 | 18.2 | 12231 | 11221 | 11221 | 11121 | 82 | 80 | 60 | 80 |
26.1_S66 | AD-CAB_3026 | RC | 79 | capsule | 26-1_S66_L001_R1_001.fastq.gz | NA | 59 | M | NA | NA | NA | Right | 176.00 | 104 | 33.70 | 2 | Ever_smoker | No | Yes | Yes | No | 2.9 | 62 | 57 | 4.2 | 3.6 | 5.3 | Yes | NA | NA | NA | NA | 30 | 42 | 44 | NA | 38.6 | 25.0 | 22.7 | NA | 12222 | 11222 | 11221 | NA | 70 | 90 | 90 | NA |
3.1_S43 | AD-CAB_3003 | RC | 55 | capsule | 3-1_S43_L001_R1_001.fastq.gz | NA | 56 | M | NA | NA | NA | Left | 179.00 | 85 | 26.52 | 1 | Never_smoker | No | Yes | NA | No | 2.9 | 72 | 90 | 4.3 | 5.2 | 5.4 | No | Intact | 50 | 50 | 100 | 38 | 38 | 44 | 48 | 29.5 | 27.3 | 9.1 | 0.0 | 11221 | 11121 | 11111 | 22222 | 80 | 70 | 80 | 60 |
4.1_S44 | AD-CAB_3004 | RC | 56 | capsule | 4-1_S44_L001_R1_001.fastq.gz | NA | 68 | M | NA | NA | NA | Right | 185.00 | 95 | 28.00 | 2 | Ever_smoker | No | Yes | Yes | No | 3.6 | 91 | 74 | 7.8 | 6.7 | 5.7 | No | Intact | 45 | 50 | 95 | 24 | 41 | 46 | 48 | NA | 18.2 | 13.6 | 0.0 | 11232 | 11121 | 11121 | 11111 | NA | 80 | 60 | 52 |
6.1_S46 | AD-CAB_3006 | RC | 58 | capsule | 6-1_S46_L001_R1_001.fastq.gz | NA | 65 | M | NA | NA | NA | Left | 172.00 | 78 | 26.00 | 1 | Never_smoker | No | No | No | No | 2.9 | 77 | 90 | 5.6 | 4.8 | 5.4 | No | Torn | NA | NA | NA | 35 | 31 | 37 | NA | 34.1 | 36.4 | 27.3 | NA | 12221 | 11221 | 11111 | NA | 82 | 40 | 80 | NA |
7.1_S47 | AD-CAB_3007 | RC | 59 | capsule | 7-1_S47_L001_R1_001.fastq.gz | NA | 63 | F | NA | NA | NA | Right | 163.00 | 57 | 21.50 | 1 | Ever_smoker | No | No | No | No | 2.9 | 53 | 90 | 29.0 | NA | 5.3 | No | Intact | 50 | 50 | 100 | 37 | 38 | 46 | 48 | 36.4 | 18.2 | 11.4 | 2.3 | 11122 | 11111 | 11111 | 11111 | 93 | 97 | 100 | 100 |
8.1_S48 | AD-CAB_3008 | RC | 60 | capsule | 8-1_S48_L001_R1_001.fastq.gz | NA | 70 | M | NA | NA | NA | Left | 167.00 | 71 | 25.50 | 2 | Never_smoker | No | Yes | Yes | No | 2.9 | 87 | 77 | 7.3 | 5.5 | 5.4 | No | Intact | NA | NA | NA | 24 | 25 | 47 | NA | 54.5 | 54.5 | 11.4 | NA | 22221 | 22221 | 11111 | NA | 90 | 90 | 92 | NA |
9.1_S49 | AD-CAB_3009 | RC | 61 | capsule | 9-1_S49_L001_R1_001.fastq.gz | NA | 68 | M | NA | NA | NA | Right | 182.00 | 83 | 25.10 | 2 | Ever_smoker | No | No | No | No | 2.9 | 79 | 88 | 7.5 | 5.8 | 5.8 | No | Intact | 50 | 50 | 100 | 35 | 41 | 43 | 46 | 52.3 | 11.4 | 4.5 | 2.3 | 11211 | 11121 | 11111 | 11111 | 85 | 96 | 90 | 90 |
plotMDS(x2c)
message("here is the model spec:")
## here is the model spec:
dds <- DESeqDataSetFromMatrix(countData = x2c , colData = ss2c, design = ~ Age + Sex + Metabolic_Syndrome )
## converting counts to integer mode
## Warning in DESeqDataSet(se, design = design, ignoreRank): some variables in
## design formula are characters, converting to factors
## the design formula contains one or more numeric variables with integer values,
## specifying a model with increasing fold change for higher values.
## did you mean for this to be a factor? if so, first convert
## this variable to a factor using the factor() function
## the design formula contains one or more numeric variables that have mean or
## standard deviation larger than 5 (an arbitrary threshold to trigger this message).
## Including numeric variables with large mean can induce collinearity with the intercept.
## Users should center and scale numeric variables in the design to improve GLM convergence.
res <- DESeq(dds)
## estimating size factors
## estimating dispersions
## gene-wise dispersion estimates
## mean-dispersion relationship
## final dispersion estimates
## fitting model and testing
z<- results(res)
vsd <- vst(dds, blind=FALSE)
zz <- cbind(as.data.frame(z),assay(vsd))
dge <- as.data.frame(zz[order(zz$pvalue),])
dge[1:20,1:6] %>%
kbl(caption = "Top DEGs in capsule between RC patients with and without metabolic syndrome.") %>%
kable_paper("hover", full_width = F)
baseMean | log2FoldChange | lfcSE | stat | pvalue | padj | |
---|---|---|---|---|---|---|
ENSG00000203812.2.H2AC18 | 15.61564 | -3.9010306 | 0.9263541 | -4.211166 | 0.0000254 | 0.4104532 |
ENSG00000197614.11.MFAP5 | 1259.04222 | -2.5068148 | 0.6332143 | -3.958872 | 0.0000753 | 0.6083095 |
ENSG00000198121.13.LPAR1 | 765.32020 | -0.6662140 | 0.1745208 | -3.817389 | 0.0001349 | 0.6255534 |
ENSG00000287286.1.AC024560.5 | 13.29192 | -3.3780136 | 0.9145029 | -3.693825 | 0.0002209 | 0.6255534 |
ENSG00000145113.22.MUC4 | 14.16622 | -1.9818044 | 0.5404158 | -3.667184 | 0.0002452 | 0.6255534 |
ENSG00000135916.16.ITM2C | 307.48864 | -1.5101725 | 0.4135695 | -3.651557 | 0.0002607 | 0.6255534 |
ENSG00000162545.6.CAMK2N1 | 75.26906 | -1.6038568 | 0.4404365 | -3.641516 | 0.0002710 | 0.6255534 |
ENSG00000267339.7.LINC00906 | 10.54983 | -2.3568631 | 0.6633982 | -3.552712 | 0.0003813 | 0.6910479 |
ENSG00000218336.9.TENM3 | 19.03004 | 1.3566231 | 0.3821275 | 3.550185 | 0.0003850 | 0.6910479 |
ENSG00000148357.16.HMCN2 | 551.37442 | -1.7044676 | 0.4899756 | -3.478679 | 0.0005039 | 0.8140891 |
ENSG00000133063.16.CHIT1 | 19.87184 | 2.6044350 | 0.7666590 | 3.397123 | 0.0006810 | 0.9999804 |
ENSG00000140254.12.DUOXA1 | 13.41342 | -1.9084883 | 0.5853997 | -3.260146 | 0.0011135 | 0.9999804 |
ENSG00000159063.14.ALG8 | 112.93939 | 0.3323802 | 0.1024597 | 3.244010 | 0.0011786 | 0.9999804 |
ENSG00000171533.12.MAP6 | 26.74399 | -1.0291686 | 0.3193044 | -3.223158 | 0.0012679 | 0.9999804 |
ENSG00000172020.13.GAP43 | 235.62709 | -1.3725239 | 0.4339196 | -3.163084 | 0.0015611 | 0.9999804 |
ENSG00000125726.11.CD70 | 38.93859 | -1.7704418 | 0.5617950 | -3.151402 | 0.0016249 | 0.9999804 |
ENSG00000149090.12.PAMR1 | 323.14328 | -2.2069636 | 0.7052207 | -3.129465 | 0.0017512 | 0.9999804 |
ENSG00000101144.13.BMP7 | 25.11222 | -1.7210234 | 0.5510064 | -3.123418 | 0.0017876 | 0.9999804 |
ENSG00000183072.10.NKX2.5 | 12.38402 | -2.2926770 | 0.7341754 | -3.122792 | 0.0017914 | 0.9999804 |
ENSG00000103540.16.CCP110 | 121.13915 | 0.2906640 | 0.0932682 | 3.116431 | 0.0018305 | 0.9999804 |
message("here is the model spec:")
## here is the model spec:
dds <- DESeqDataSetFromMatrix(countData = x2c , colData = ss2c, design = ~ Age + Sex + CRP + Metabolic_Syndrome )
## converting counts to integer mode
## Warning in DESeqDataSet(se, design = design, ignoreRank): some variables in
## design formula are characters, converting to factors
## the design formula contains one or more numeric variables with integer values,
## specifying a model with increasing fold change for higher values.
## did you mean for this to be a factor? if so, first convert
## this variable to a factor using the factor() function
## the design formula contains one or more numeric variables that have mean or
## standard deviation larger than 5 (an arbitrary threshold to trigger this message).
## Including numeric variables with large mean can induce collinearity with the intercept.
## Users should center and scale numeric variables in the design to improve GLM convergence.
res <- DESeq(dds)
## estimating size factors
## estimating dispersions
## gene-wise dispersion estimates
## mean-dispersion relationship
## final dispersion estimates
## fitting model and testing
z<- results(res)
vsd <- vst(dds, blind=FALSE)
zz <- cbind(as.data.frame(z),assay(vsd))
dge <- as.data.frame(zz[order(zz$pvalue),])
dge[1:20,1:6] %>%
kbl(caption = "Top DEGs in bone between OA patients with and without metabolic syndrome, adjusted for age, sex and CRP.") %>%
kable_paper("hover", full_width = F)
baseMean | log2FoldChange | lfcSE | stat | pvalue | padj | |
---|---|---|---|---|---|---|
ENSG00000203812.2.H2AC18 | 15.61564 | -4.4182659 | 1.0336522 | -4.274422 | 0.0000192 | 0.3098525 |
ENSG00000135480.16.KRT7 | 26.26632 | -2.0953587 | 0.5318943 | -3.939427 | 0.0000817 | 0.4412672 |
ENSG00000198121.13.LPAR1 | 765.32020 | -0.7242177 | 0.1843492 | -3.928510 | 0.0000855 | 0.4412672 |
ENSG00000260266.1.PPIAP46 | 28.56331 | 1.4338041 | 0.3726096 | 3.848006 | 0.0001191 | 0.4412672 |
ENSG00000133063.16.CHIT1 | 19.87184 | 2.9820708 | 0.7914467 | 3.767873 | 0.0001646 | 0.4412672 |
ENSG00000181634.8.TNFSF15 | 99.83771 | 1.4552388 | 0.3889060 | 3.741878 | 0.0001827 | 0.4412672 |
ENSG00000109472.14.CPE | 197.99383 | 1.2409169 | 0.3326334 | 3.730584 | 0.0001910 | 0.4412672 |
ENSG00000197614.11.MFAP5 | 1259.04222 | -2.4854321 | 0.6815676 | -3.646641 | 0.0002657 | 0.5369949 |
ENSG00000218336.9.TENM3 | 19.03004 | 1.4454954 | 0.4010120 | 3.604619 | 0.0003126 | 0.5616232 |
ENSG00000181195.11.PENK | 41.98586 | 2.5020799 | 0.7244314 | 3.453854 | 0.0005526 | 0.8356607 |
ENSG00000162545.6.CAMK2N1 | 75.26906 | -1.6312015 | 0.4761735 | -3.425645 | 0.0006133 | 0.8356607 |
ENSG00000148357.16.HMCN2 | 551.37442 | -1.7818720 | 0.5227430 | -3.408696 | 0.0006527 | 0.8356607 |
ENSG00000274422.1.AC245060.5 | 487.41427 | 1.4959447 | 0.4407833 | 3.393832 | 0.0006892 | 0.8356607 |
ENSG00000183688.4.RFLNB | 145.76873 | -1.6084987 | 0.4758178 | -3.380492 | 0.0007236 | 0.8356607 |
ENSG00000267339.7.LINC00906 | 10.54983 | -2.4460215 | 0.7334720 | -3.334853 | 0.0008534 | 0.8662717 |
ENSG00000135916.16.ITM2C | 307.48864 | -1.4756737 | 0.4451913 | -3.314696 | 0.0009174 | 0.8662717 |
ENSG00000124214.21.STAU1 | 498.95136 | -0.2358579 | 0.0711775 | -3.313658 | 0.0009208 | 0.8662717 |
ENSG00000159063.14.ALG8 | 112.93939 | 0.3588266 | 0.1087116 | 3.300720 | 0.0009644 | 0.8662717 |
ENSG00000169071.15.ROR2 | 25.21287 | 2.1959724 | 0.6696037 | 3.279511 | 0.0010399 | 0.8849324 |
ENSG00000145113.22.MUC4 | 14.16622 | -1.8667078 | 0.5818057 | -3.208473 | 0.0013344 | 0.9499071 |
dge2c <- dge
For reproducibility.
sessionInfo()
## R version 4.3.1 (2023-06-16)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 22.04.3 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
##
## locale:
## [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8
## [5] LC_MONETARY=en_AU.UTF-8 LC_MESSAGES=en_AU.UTF-8
## [7] LC_PAPER=en_AU.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C
##
## time zone: Australia/Melbourne
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats4 stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] pkgload_1.3.2.1 GGally_2.1.2
## [3] beeswarm_0.4.0 gtools_3.9.4
## [5] echarts4r_0.4.5 kableExtra_1.3.4
## [7] topconfects_1.16.0 limma_3.56.2
## [9] eulerr_7.0.0 mitch_1.12.0
## [11] MASS_7.3-60 fgsea_1.26.0
## [13] gplots_3.1.3 DESeq2_1.40.2
## [15] SummarizedExperiment_1.30.2 Biobase_2.60.0
## [17] MatrixGenerics_1.12.3 matrixStats_1.0.0
## [19] GenomicRanges_1.52.0 GenomeInfoDb_1.36.3
## [21] IRanges_2.34.1 S4Vectors_0.38.1
## [23] BiocGenerics_0.46.0 reshape2_1.4.4
## [25] lubridate_1.9.2 forcats_1.0.0
## [27] stringr_1.5.0 dplyr_1.1.3
## [29] purrr_1.0.2 readr_2.1.4
## [31] tidyr_1.3.0 tibble_3.2.1
## [33] ggplot2_3.4.3 tidyverse_2.0.0
## [35] zoo_1.8-12 R.utils_2.12.2
## [37] R.oo_1.25.0 R.methodsS3_1.8.2
##
## loaded via a namespace (and not attached):
## [1] bitops_1.0-7 gridExtra_2.3 rlang_1.1.1
## [4] magrittr_2.0.3 compiler_4.3.1 systemfonts_1.0.4
## [7] vctrs_0.6.3 rvest_1.0.3 pkgconfig_2.0.3
## [10] crayon_1.5.2 fastmap_1.1.1 XVector_0.40.0
## [13] ellipsis_0.3.2 caTools_1.18.2 utf8_1.2.3
## [16] promises_1.2.1 rmarkdown_2.24 tzdb_0.4.0
## [19] xfun_0.40 zlibbioc_1.46.0 cachem_1.0.8
## [22] jsonlite_1.8.7 highr_0.10 later_1.3.1
## [25] DelayedArray_0.26.7 reshape_0.8.9 BiocParallel_1.34.2
## [28] parallel_4.3.1 R6_2.5.1 bslib_0.5.1
## [31] stringi_1.7.12 RColorBrewer_1.1-3 jquerylib_0.1.4
## [34] assertthat_0.2.1 Rcpp_1.0.11 knitr_1.44
## [37] httpuv_1.6.11 Matrix_1.6-1 timechange_0.2.0
## [40] tidyselect_1.2.0 rstudioapi_0.15.0 abind_1.4-5
## [43] yaml_2.3.7 codetools_0.2-19 lattice_0.21-8
## [46] plyr_1.8.8 shiny_1.7.5 withr_2.5.0
## [49] evaluate_0.21 xml2_1.3.5 pillar_1.9.0
## [52] KernSmooth_2.23-22 generics_0.1.3 RCurl_1.98-1.12
## [55] hms_1.1.3 munsell_0.5.0 scales_1.2.1
## [58] xtable_1.8-4 glue_1.6.2 tools_4.3.1
## [61] data.table_1.14.8 webshot_0.5.5 locfit_1.5-9.8
## [64] fastmatch_1.1-4 cowplot_1.1.1 grid_4.3.1
## [67] colorspace_2.1-0 GenomeInfoDbData_1.2.10 cli_3.6.1
## [70] fansi_1.0.4 viridisLite_0.4.2 S4Arrays_1.0.6
## [73] svglite_2.1.1 gtable_0.3.4 sass_0.4.7
## [76] digest_0.6.33 htmlwidgets_1.6.2 htmltools_0.5.6
## [79] lifecycle_1.0.3 httr_1.4.7 mime_0.12