Shoulder transcriptome analysis: rotator cuff repair

Import count data and sample sheet

caps_rcr= capsule rotator cuff repair.

caps_oa= capsule of primary OA

caps_rca= capsule rotator cuff arthropathy

caps_all= includes all three above groups.

x <- readRDS("counts.rds")

ss <- read.table("samplesheets/pheno_data.tsv",header=TRUE)
head(ss,3)

##   Participant_ID Case Redcap_ID Tissue                    fastq pvt.pub Age Sex
## 1    AD-CAB_4001   OA        84   bone 4001-41B_R1_001.fastq.gz     pvt  69   F
## 2    AD-CAB_4002   OA        80   bone 4002-42B_R1_001.fastq.gz     pvt  59   M
## 3    AD-CAB_4003   OA        81   bone 4003-43B_R1_001.fastq.gz     pvt  74   F
##   Primary_OA Cuff_Arthropathy Prosthesis Affected_Side Height_cm Weight_kg BMI
## 1        Yes               No   Anatomic          Left       158        89  36
## 2        Yes               No   Anatomic          Left       182       106  32
## 3         No              Yes    Reverse         Right       153        87  37
##   ASA      Smoking Diabetes Hypercholesterolaemia Hypertension Thyroid CRP
## 1   2 Never_smoker       No                   Yes          Yes     Yes 2.9
## 2   1  Ever_smoker       No                   Yes           No      No 9.3
## 3   2  Ever_smoker       No                   Yes          Yes      No 6.9
##   Creat eGFR Urea Fast_Glucose hba1c Metabolic_Syndrome
## 1    66   82  5.2          5.7   6.1                Yes
## 2    69   90  4.3          6.2   5.4                Yes
## 3    77   66  5.0          5.4   5.4                Yes
##   Tendon_integrity_2_years_post.op ASES_2_years_post.op_Pain
## 1                             <NA>                        NA
## 2                             <NA>                        NA
## 3                             <NA>                        NA
##   ASES_2_years_post.op_ADL ASES_2_years_post.op_Total Oxford_Baseline
## 1                       NA                         NA              NA
## 2                       NA                         NA              NA
## 3                       NA                         NA              NA
##   Oxford_3_month Oxford_12_month Oxford_24_month QuickDASH_ QuickDASH_3_month
## 1             NA              NA              NA         NA                NA
## 2             NA              NA              NA         NA                NA
## 3             NA              NA              NA         NA                NA
##   QuickDASH_12_month QuickDASH_24_month EQ.5D.3L_Baseline EQ.5D.3L_3_month
## 1                 NA                 NA                NA               NA
## 2                 NA                 NA                NA               NA
## 3                 NA                 NA                NA               NA
##   EQ.5D.3L_12_month EQ.5D.3L_24_month EQVAS_Baseline EQVAS_3_month
## 1                NA                NA             NA            NA
## 2                NA                NA             NA            NA
## 3                NA                NA             NA            NA
##   EQVAS_12_month EQVAS_24_month
## 1             NA             NA
## 2             NA             NA
## 3             NA             NA

sapply(strsplit(gsub("-",".",gsub("_L001","|",gsub("_R1","|",ss$fastq))),"\\|"),"[[",1) %in% colnames(x)

##   [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
##  [16] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
##  [31] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
##  [46] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
##  [61] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
##  [76] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
##  [91] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
## [106] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
## [121] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
## [136] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
## [151] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE

ss$data <- sapply(strsplit(gsub("-",".",gsub("_L001","|",gsub("_R1","|",ss$fastq))),"\\|"),"[[",1) 

rownames(ss)<-ss$data

caps <- subset(ss,Tissue=="capsule")
head(caps,2)

##          Participant_ID Case Redcap_ID  Tissue                    fastq pvt.pub
## 4001.41C    AD-CAB_4001   OA        84 capsule 4001-41C_R1_001.fastq.gz     pvt
## 4002.42C    AD-CAB_4002   OA        80 capsule 4002-42C_R1_001.fastq.gz     pvt
##          Age Sex Primary_OA Cuff_Arthropathy Prosthesis Affected_Side Height_cm
## 4001.41C  69   F        Yes               No   Anatomic          Left       158
## 4002.42C  59   M        Yes               No   Anatomic          Left       182
##          Weight_kg BMI ASA      Smoking Diabetes Hypercholesterolaemia
## 4001.41C        89  36   2 Never_smoker       No                   Yes
## 4002.42C       106  32   1  Ever_smoker       No                   Yes
##          Hypertension Thyroid CRP Creat eGFR Urea Fast_Glucose hba1c
## 4001.41C          Yes     Yes 2.9    66   82  5.2          5.7   6.1
## 4002.42C           No      No 9.3    69   90  4.3          6.2   5.4
##          Metabolic_Syndrome Tendon_integrity_2_years_post.op
## 4001.41C                Yes                             <NA>
## 4002.42C                Yes                             <NA>
##          ASES_2_years_post.op_Pain ASES_2_years_post.op_ADL
## 4001.41C                        NA                       NA
## 4002.42C                        NA                       NA
##          ASES_2_years_post.op_Total Oxford_Baseline Oxford_3_month
## 4001.41C                         NA              NA             NA
## 4002.42C                         NA              NA             NA
##          Oxford_12_month Oxford_24_month QuickDASH_ QuickDASH_3_month
## 4001.41C              NA              NA         NA                NA
## 4002.42C              NA              NA         NA                NA
##          QuickDASH_12_month QuickDASH_24_month EQ.5D.3L_Baseline
## 4001.41C                 NA                 NA                NA
## 4002.42C                 NA                 NA                NA
##          EQ.5D.3L_3_month EQ.5D.3L_12_month EQ.5D.3L_24_month EQVAS_Baseline
## 4001.41C               NA                NA                NA             NA
## 4002.42C               NA                NA                NA             NA
##          EQVAS_3_month EQVAS_12_month EQVAS_24_month     data
## 4001.41C            NA             NA             NA 4001.41C
## 4002.42C            NA             NA             NA 4002.42C

dim(caps)

## [1] 72 49

caps_rcr <- caps[grep("_30",caps$Participant_ID),]
head(caps_rcr,3)

##         Participant_ID Case Redcap_ID  Tissue                        fastq
## 1.1_S41    AD-CAB_3001   RC        53 capsule 1-1_S41_L001_R1_001.fastq.gz
## 2.1_S42    AD-CAB_3002   RC        54 capsule 2-1_S42_L001_R1_001.fastq.gz
## 3.1_S43    AD-CAB_3003   RC        55 capsule 3-1_S43_L001_R1_001.fastq.gz
##         pvt.pub Age Sex Primary_OA Cuff_Arthropathy Prosthesis Affected_Side
## 1.1_S41    <NA>  67   M       <NA>             <NA>       <NA>          Left
## 2.1_S42    <NA>  58   M       <NA>             <NA>       <NA>         Right
## 3.1_S43    <NA>  56   M       <NA>             <NA>       <NA>          Left
##         Height_cm Weight_kg   BMI ASA      Smoking Diabetes
## 1.1_S41     177.8       120 37.90   2  Ever_smoker       No
## 2.1_S42     179.0        79 25.00   1 Never_smoker       No
## 3.1_S43     179.0        85 26.52   1 Never_smoker       No
##         Hypercholesterolaemia Hypertension Thyroid CRP Creat eGFR Urea
## 1.1_S41                   Yes          Yes      No 2.9    83   84  7.0
## 2.1_S42                    No           No      No 0.7    70   90  6.9
## 3.1_S43                   Yes         <NA>      No 2.9    72   90  4.3
##         Fast_Glucose hba1c Metabolic_Syndrome Tendon_integrity_2_years_post.op
## 1.1_S41          5.2   5.6                Yes                             Torn
## 2.1_S42          5.4   5.3                 No                             Torn
## 3.1_S43          5.2   5.4                 No                           Intact
##         ASES_2_years_post.op_Pain ASES_2_years_post.op_ADL
## 1.1_S41                        NA                       NA
## 2.1_S42                        NA                       NA
## 3.1_S43                        50                       50
##         ASES_2_years_post.op_Total Oxford_Baseline Oxford_3_month
## 1.1_S41                         NA              25             41
## 2.1_S42                         NA              33             NA
## 3.1_S43                        100              38             38
##         Oxford_12_month Oxford_24_month QuickDASH_ QuickDASH_3_month
## 1.1_S41              46              NA       38.6              13.6
## 2.1_S42              48              NA       29.5                NA
## 3.1_S43              44              48       29.5              27.3
##         QuickDASH_12_month QuickDASH_24_month EQ.5D.3L_Baseline
## 1.1_S41               13.6                 NA             11222
## 2.1_S42                0.0                 NA             11111
## 3.1_S43                9.1                  0             11221
##         EQ.5D.3L_3_month EQ.5D.3L_12_month EQ.5D.3L_24_month EQVAS_Baseline
## 1.1_S41            11123             21222                NA             90
## 2.1_S42               NA             11111                NA             90
## 3.1_S43            11121             11111             22222             80
##         EQVAS_3_month EQVAS_12_month EQVAS_24_month    data
## 1.1_S41            50             60             NA 1.1_S41
## 2.1_S42            NA             90             NA 2.1_S42
## 3.1_S43            70             80             60 3.1_S43

dim(caps_rcr)

## [1] 26 49

caps_rcr$group="rcr"
caps_rcr %>% kbl(caption = "Capsule samples of rotator cuff repair group") %>% kable_paper("hover", full_width = F)

Capsule samples of rotator cuff repair group
	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	data	group
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	1.1_S41	rcr
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	2.1_S42	rcr
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	3.1_S43	rcr
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	4.1_S44	rcr
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	5.1_S45	rcr
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	6.1_S46	rcr
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	7.1_S47	rcr
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	8.1_S48	rcr
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	9.1_S49	rcr
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	10.1_S50	rcr
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	11.1_S51	rcr
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	12.1_S52	rcr
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	13.1_S53	rcr
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	14.1_S54	rcr
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	15.1_S55	rcr
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	16.1_S56	rcr
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	17.1_S57	rcr
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	18.1_S58	rcr
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	19.1_S59	rcr
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	20.1_S60	rcr
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	21.1_S61	rcr
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	22.1_S62	rcr
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	23.1_S63	rcr
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	24.1_S64	rcr
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	25.1_S65	rcr
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	26.1_S66	rcr

caps_oa <- subset(caps,Primary_OA=="Yes")
head(caps_oa,3)

##          Participant_ID Case Redcap_ID  Tissue                    fastq pvt.pub
## 4001.41C    AD-CAB_4001   OA        84 capsule 4001-41C_R1_001.fastq.gz     pvt
## 4002.42C    AD-CAB_4002   OA        80 capsule 4002-42C_R1_001.fastq.gz     pvt
## 4004.44C    AD-CAB_4004   OA        82 capsule 4004-44C_R1_001.fastq.gz     pvt
##          Age Sex Primary_OA Cuff_Arthropathy Prosthesis Affected_Side Height_cm
## 4001.41C  69   F        Yes               No   Anatomic          Left       158
## 4002.42C  59   M        Yes               No   Anatomic          Left       182
## 4004.44C  69   F        Yes               No   Anatomic          Left       165
##          Weight_kg BMI ASA      Smoking Diabetes Hypercholesterolaemia
## 4001.41C        89  36   2 Never_smoker       No                   Yes
## 4002.42C       106  32   1  Ever_smoker       No                   Yes
## 4004.44C        85  32   2 Never_smoker       No                   Yes
##          Hypertension Thyroid CRP Creat eGFR Urea Fast_Glucose hba1c
## 4001.41C          Yes     Yes 2.9    66   82  5.2          5.7   6.1
## 4002.42C           No      No 9.3    69   90  4.3          6.2   5.4
## 4004.44C          Yes     Yes 3.9    61   89  5.8          5.8   5.6
##          Metabolic_Syndrome Tendon_integrity_2_years_post.op
## 4001.41C                Yes                             <NA>
## 4002.42C                Yes                             <NA>
## 4004.44C                Yes                             <NA>
##          ASES_2_years_post.op_Pain ASES_2_years_post.op_ADL
## 4001.41C                        NA                       NA
## 4002.42C                        NA                       NA
## 4004.44C                        NA                       NA
##          ASES_2_years_post.op_Total Oxford_Baseline Oxford_3_month
## 4001.41C                         NA              NA             NA
## 4002.42C                         NA              NA             NA
## 4004.44C                         NA              NA             NA
##          Oxford_12_month Oxford_24_month QuickDASH_ QuickDASH_3_month
## 4001.41C              NA              NA         NA                NA
## 4002.42C              NA              NA         NA                NA
## 4004.44C              NA              NA         NA                NA
##          QuickDASH_12_month QuickDASH_24_month EQ.5D.3L_Baseline
## 4001.41C                 NA                 NA                NA
## 4002.42C                 NA                 NA                NA
## 4004.44C                 NA                 NA                NA
##          EQ.5D.3L_3_month EQ.5D.3L_12_month EQ.5D.3L_24_month EQVAS_Baseline
## 4001.41C               NA                NA                NA             NA
## 4002.42C               NA                NA                NA             NA
## 4004.44C               NA                NA                NA             NA
##          EQVAS_3_month EQVAS_12_month EQVAS_24_month     data
## 4001.41C            NA             NA             NA 4001.41C
## 4002.42C            NA             NA             NA 4002.42C
## 4004.44C            NA             NA             NA 4004.44C

dim(caps_oa)

## [1] 16 49

caps_oa$group="oa"
caps_oa %>% kbl(caption = "Capsule samples of primary OA group") %>% kable_paper("hover", full_width = F)

Capsule samples of primary OA group
	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	data	group
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	4001.41C	oa
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	4002.42C	oa
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	4004.44C	oa
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	4005.45C	oa
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	4006.46C	oa
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	7C_S32	oa
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	8C_S33	oa
11C_S36	AD-CAB_4011	OA	87	capsule	11C_S36_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	11C_S36	oa
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	12C_S37	oa
14C_S39	AD-CAB_4014	OA	92	capsule	14C_S39_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	14C_S39	oa
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	15C_S40	oa
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	16C_S41	oa
17C_S42	AD-CAB_4017	OA	96	capsule	17C_S42_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	17C_S42	oa
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	18C_S43	oa
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	19C_S44	oa
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	20C_S45	oa

caps_rca <- subset(caps,Cuff_Arthropathy=="Yes")
head(caps_rca,3)

##          Participant_ID Case Redcap_ID  Tissue                        fastq
## 4003.43C    AD-CAB_4003   OA        81 capsule     4003-43C_R1_001.fastq.gz
## 9C_S34      AD-CAB_4009   OA        88 capsule  9C_S34_L001_R1_001.fastq.gz
## 10C_S35     AD-CAB_4010   OA        90 capsule 10C_S35_L001_R1_001.fastq.gz
##          pvt.pub Age Sex Primary_OA Cuff_Arthropathy Prosthesis Affected_Side
## 4003.43C     pvt  74   F         No              Yes    Reverse         Right
## 9C_S34       pvt  72   M         No              Yes    Reverse         Right
## 10C_S35      pvt  80   F         No              Yes    Reverse          Left
##          Height_cm Weight_kg BMI ASA      Smoking Diabetes
## 4003.43C       153        87  37   2  Ever_smoker       No
## 9C_S34         167        80  29   3  Ever_smoker       No
## 10C_S35        161        72  28   2 Never_smoker       No
##          Hypercholesterolaemia Hypertension Thyroid  CRP Creat eGFR Urea
## 4003.43C                   Yes          Yes      No  6.9    77   66  5.0
## 9C_S34                     Yes          Yes      No  2.9   107   59  6.7
## 10C_S35                    Yes           No     Yes 11.2    54   86  8.5
##          Fast_Glucose hba1c Metabolic_Syndrome Tendon_integrity_2_years_post.op
## 4003.43C          5.4   5.4                Yes                             <NA>
## 9C_S34            5.8   5.5                 No                             <NA>
## 10C_S35           7.3   5.6                 No                             <NA>
##          ASES_2_years_post.op_Pain ASES_2_years_post.op_ADL
## 4003.43C                        NA                       NA
## 9C_S34                          NA                       NA
## 10C_S35                         NA                       NA
##          ASES_2_years_post.op_Total Oxford_Baseline Oxford_3_month
## 4003.43C                         NA              NA             NA
## 9C_S34                           NA              NA             NA
## 10C_S35                          NA              NA             NA
##          Oxford_12_month Oxford_24_month QuickDASH_ QuickDASH_3_month
## 4003.43C              NA              NA         NA                NA
## 9C_S34                NA              NA         NA                NA
## 10C_S35               NA              NA         NA                NA
##          QuickDASH_12_month QuickDASH_24_month EQ.5D.3L_Baseline
## 4003.43C                 NA                 NA                NA
## 9C_S34                   NA                 NA                NA
## 10C_S35                  NA                 NA                NA
##          EQ.5D.3L_3_month EQ.5D.3L_12_month EQ.5D.3L_24_month EQVAS_Baseline
## 4003.43C               NA                NA                NA             NA
## 9C_S34                 NA                NA                NA             NA
## 10C_S35                NA                NA                NA             NA
##          EQVAS_3_month EQVAS_12_month EQVAS_24_month     data
## 4003.43C            NA             NA             NA 4003.43C
## 9C_S34              NA             NA             NA   9C_S34
## 10C_S35             NA             NA             NA  10C_S35

dim(caps_rca)

## [1]  4 49

caps_rca$group="rca"
caps_rca %>% kbl(caption = "Capsule samples of rotator cuff arthropathy group") %>% kable_paper("hover", full_width = F)

Capsule samples of rotator cuff arthropathy group
	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	data	group
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	4003.43C	rca
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	9C_S34	rca
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	10C_S35	rca
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	13C_S38	rca

caps_all <- rbind(caps_rcr,caps_oa,caps_rca)

xcaps <- x[,which(colnames(x) %in% rownames(caps_all) )]

dim(xcaps)

## [1] 60651    46

dim(caps_all) # matches OK

## [1] 46 50

caps_all %>% kbl(caption = "Capsule samples") %>% kable_paper("hover", full_width = F)

Capsule samples
	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	data	group
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	1.1_S41	rcr
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	2.1_S42	rcr
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	3.1_S43	rcr
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	4.1_S44	rcr
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	5.1_S45	rcr
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	6.1_S46	rcr
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	7.1_S47	rcr
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	8.1_S48	rcr
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	9.1_S49	rcr
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	10.1_S50	rcr
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	11.1_S51	rcr
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	12.1_S52	rcr
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	13.1_S53	rcr
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	14.1_S54	rcr
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	15.1_S55	rcr
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	16.1_S56	rcr
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	17.1_S57	rcr
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	18.1_S58	rcr
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	19.1_S59	rcr
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	20.1_S60	rcr
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	21.1_S61	rcr
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	22.1_S62	rcr
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	23.1_S63	rcr
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	24.1_S64	rcr
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	25.1_S65	rcr
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	26.1_S66	rcr
4001.41C	AD-CAB_4001	OA	84	capsule	4001-41C_R1_001.fastq.gz	pvt	69	F	Yes	No	Anatomic	Left	158.00	89	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	oa
4002.42C	AD-CAB_4002	OA	80	capsule	4002-42C_R1_001.fastq.gz	pvt	59	M	Yes	No	Anatomic	Left	182.00	106	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	oa
4004.44C	AD-CAB_4004	OA	82	capsule	4004-44C_R1_001.fastq.gz	pvt	69	F	Yes	No	Anatomic	Left	165.00	85	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	oa
4005.45C	AD-CAB_4005	OA	83	capsule	4005-45C_R1_001.fastq.gz	pvt	74	F	Yes	No	Anatomic	Left	169.00	75	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	oa
4006.46C	AD-CAB_4006	OA	78	capsule	4006-46C_R1_001.fastq.gz	pvt	81	F	Yes	No	Anatomic	Right	150.00	54	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	oa
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	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	oa
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	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	oa
11C_S36	AD-CAB_4011	OA	87	capsule	11C_S36_L001_R1_001.fastq.gz	pub	76	M	Yes	No	Reverse	Right	180.00	92	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	oa
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	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	oa
14C_S39	AD-CAB_4014	OA	92	capsule	14C_S39_L001_R1_001.fastq.gz	pvt	71	M	Yes	No	Reverse	Right	170.00	99	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	oa
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	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	oa
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	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	oa
17C_S42	AD-CAB_4017	OA	96	capsule	17C_S42_L001_R1_001.fastq.gz	pvt	79	F	Yes	No	Reverse	Right	155.00	75	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	oa
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	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	oa
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	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	oa
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	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	oa
4003.43C	AD-CAB_4003	OA	81	capsule	4003-43C_R1_001.fastq.gz	pvt	74	F	No	Yes	Reverse	Right	153.00	87	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	rca
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	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	rca
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	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	rca
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	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	rca

QC analysis

First to look at the number of reads per data set.

par(mar=c(5,8,3,1))
barplot(colSums(xcaps),horiz=TRUE,las=1,xlab="Capsule reads")

sums <- colSums(xcaps)
sums <- sums[order(sums)]
barplot(sums,horiz=TRUE,las=1,xlab="Capsule reads")
abline(v=15000000,col="red")

MDS plot

Multidimensional scaling plot to show the variation between all samples, very similar to PCA.

mds <- cmdscale(dist(t(xcaps)))

plot(mds, xlab="Coordinate 1", ylab="Coordinate 2",
  type = "p",bty="n",pch=19, cex=4 ,col="gray")
text(mds, labels=rownames(mds) )

rcr1 <- as.numeric(colnames(xcaps) %in% rownames(caps_rcr))*1
oa2 <- as.numeric(colnames(xcaps) %in% rownames(caps_oa))*2
rca3 <- as.numeric(colnames(xcaps) %in% rownames(caps_rca))*3

mycols <- gsub("3","gray",gsub("2","pink",gsub("1","lightblue",as.character(rcr1+oa2+rca3))))

plot(mds, xlab="Coordinate 1", ylab="Coordinate 2",
  type = "p",bty="n",pch=19, cex=4 ,col=mycols)
text(mds, labels=rownames(mds) )
mtext("RCR=lightblue, OA=pink, RCA=grey")

Prep pathways

genesets <- gmt_import("ReactomePathways_2023-09-01.gmt")

# gene table
gt <- as.data.frame(rownames(x))
#gt$gene <- sapply(strsplit(gt[,1]," "),"[[",2)
gt[,1] <- sub("@",".",sub("\\."," ",(sub("\\.","@",gt[,1]))))
gt$gene <- sapply(strsplit(gt[,1]," "),"[[",2)
gt[,1] <- rownames(x)

Primary OA vs Rotator cuff arthropathy

ss1 <- rbind(caps_oa,caps_rca)
ss1 <- ss1[order(rownames(ss1)),]

x1 <- xcaps[,colnames(xcaps) %in% rownames(ss1)]
x1 <- x1[,order(colnames(x1)),]

colnames(x1) == rownames(ss1)

##  [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
## [16] TRUE TRUE TRUE TRUE TRUE

x1f <- x1[which(rowMeans(x1)>10),]
dim(x1)

## [1] 60651    20

dim(x1f)

## [1] 17320    20

dds <- DESeqDataSetFromMatrix(countData = x1f , colData = ss1, design = ~ Age +Sex + Cuff_Arthropathy )

## 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),])
head(dge,20) %>%
  kbl(caption = "Top gene expression differences between OA (ctrl) and Rotator cuff arthropathy (case)") %>%
  kable_paper("hover", full_width = F)

Top gene expression differences between OA (ctrl) and Rotator cuff arthropathy (case)
	baseMean	log2FoldChange	lfcSE	stat	pvalue	padj	10C_S35	11C_S36	12C_S37	13C_S38	14C_S39	15C_S40	16C_S41	17C_S42	18C_S43	19C_S44	20C_S45	4001.41C	4002.42C	4003.43C	4004.44C	4005.45C	4006.46C	7C_S32	8C_S33	9C_S34
ENSG00000237541.4.HLA.DQA2	260.110807	-5.7542931	1.1206766	-5.134660	0.0000003	0.0048956	4.886017	5.047695	8.701297	4.739816	9.447974	8.862121	6.666200	10.131204	7.439342	7.469456	6.966987	7.849253	7.647561	4.329657	7.306233	8.021589	4.550543	9.591056	9.642943	6.059449
ENSG00000133063.16.CHIT1	316.413226	5.7790813	1.1636789	4.966216	0.0000007	0.0059123	6.211761	7.704650	5.394606	5.464211	8.269533	6.024971	5.739692	6.356210	6.347096	5.571036	6.075669	4.948037	8.106576	12.385902	5.808181	5.111196	5.768824	5.440711	5.170406	5.202797
ENSG00000275464.5.FP565260.1	204.636968	-1.1807921	0.2449152	-4.821229	0.0000014	0.0082372	7.083534	7.330945	8.434623	6.950281	8.055274	7.734842	8.285886	8.426757	8.366033	7.842061	7.590137	8.409162	7.924618	7.152445	7.804173	7.704498	7.813557	8.285409	8.467569	7.304273
ENSG00000002745.13.WNT16	38.840675	4.2957828	0.9442171	4.549571	0.0000054	0.0232761	6.520765	4.329657	4.329657	9.383508	5.094109	4.329657	4.880711	4.689958	4.864712	5.302621	4.873308	4.688492	5.258311	5.354730	5.072126	5.990612	4.868113	4.688822	4.329657	5.202797
ENSG00000229391.7.HLA.DRB6	38.352617	-3.5605721	0.8021207	-4.438948	0.0000090	0.0313144	5.008993	4.839979	6.582845	4.329657	6.751347	6.484565	5.641965	7.149764	6.373227	6.063562	6.401728	6.163247	6.194656	4.735771	5.349321	6.615720	4.711501	6.931740	6.801082	5.415188
ENSG00000101198.15.NKAIN4	10.813567	-3.2944360	0.7653338	-4.304574	0.0000167	0.0482961	4.329657	5.840759	5.685480	4.739816	5.209055	5.467214	4.880711	5.268737	5.654565	5.401022	5.625241	5.571372	5.691091	4.587013	5.309242	5.719665	4.987255	5.541145	4.928301	4.906181
ENSG00000280411.1.IGHV1.69D	12.480475	-5.7748090	1.3582000	-4.251810	0.0000212	0.0524671	4.329657	4.329657	5.394606	4.739816	5.918871	4.680731	6.195769	5.905537	5.168638	4.985013	4.329657	4.792124	4.725299	4.329657	5.099518	6.719868	5.579444	6.146381	4.676930	4.329657
ENSG00000172602.11.RND1	46.190425	2.6005315	0.6213823	4.185075	0.0000285	0.0612747	8.630991	6.265003	5.726806	6.514488	6.580533	6.082192	6.130897	5.127215	5.788727	5.749688	6.744568	5.286273	5.930144	5.578762	5.604564	5.044521	5.200771	6.374027	5.633103	6.453955
ENSG00000205054.8.LINC01121	10.113086	2.0669291	0.4968712	4.159889	0.0000318	0.0612747	5.601000	5.596432	4.691803	6.243837	4.774432	4.824941	5.412854	5.044789	5.317017	5.248834	4.993563	5.012165	5.010736	5.453485	5.245327	5.008515	5.022175	5.124749	5.019296	6.059449
ENSG00000280071.4.GATD3B	468.236776	-0.7197878	0.1826198	-3.941456	0.0000810	0.1402719	9.220647	8.784552	9.303387	8.099893	8.948378	9.094952	9.566582	9.116585	9.269716	8.952068	8.731232	8.997821	9.052475	8.262399	8.885076	9.247737	8.929471	9.203230	9.007683	8.203705
ENSG00000211644.3.IGLV1.51	8.002484	-5.3084911	1.3556423	-3.915849	0.0000901	0.1418452	4.329657	4.329657	4.691803	4.329657	4.956221	4.329657	5.104369	5.389386	5.830020	5.248834	5.674673	4.537186	4.887453	4.511756	5.072126	6.189200	5.878898	5.386169	4.819604	4.329657
ENSG00000168010.11.ATG16L2	616.884160	-0.8038562	0.2070006	-3.883352	0.0001030	0.1450043	8.614326	9.094488	9.551476	8.286163	10.304948	9.572188	9.015437	9.280737	8.980726	9.345596	9.603424	9.364020	10.075704	8.858129	9.781076	9.522612	9.022952	9.332323	9.303665	8.691548
ENSG00000160221.18.GATD3A	82.778829	2.6174458	0.6763432	3.869996	0.0001088	0.1450043	5.926352	8.377775	5.979610	8.402775	6.419102	5.515178	5.641965	6.151497	5.082125	5.749688	6.427594	5.910968	5.723966	8.105793	5.731305	7.026018	5.838875	5.675012	5.885891	8.581185
ENSG00000103507.14.BCKDK	275.789567	-0.6994989	0.1850484	-3.780086	0.0001568	0.1939519	7.951191	8.554545	8.306499	7.645144	8.455838	8.068535	8.479004	8.468568	8.544727	8.006073	8.012512	8.585949	8.659730	7.804080	8.404579	8.936205	8.284902	8.170391	8.021933	7.861898
ENSG00000166233.15.ARIH1	389.566025	0.4240808	0.1133701	3.740676	0.0001835	0.2027201	9.183525	8.583597	8.450521	9.132993	8.837118	8.615369	8.701681	8.499144	8.384333	8.833378	8.741029	8.727771	8.681334	8.797936	8.780207	8.508204	8.758744	8.777735	8.573640	9.016163
ENSG00000105639.20.JAK3	216.338437	-0.9913523	0.2658921	-3.728402	0.0001927	0.2027201	6.706876	8.176070	7.389891	7.133563	8.965184	8.074988	7.289153	7.960700	8.175908	7.641284	8.136852	7.864931	8.498648	6.840915	8.205246	8.052215	8.330243	8.465532	7.884797	8.051943
ENSG00000228021.7.AL158835.1	31.291981	3.2610502	0.8765522	3.720315	0.0001990	0.2027201	7.209350	5.641254	4.953684	7.520695	7.448468	5.467214	5.412854	5.127215	5.554552	4.898414	6.841707	4.980944	4.653033	5.093787	4.949491	4.723993	5.117042	6.173822	5.296095	5.505013
ENSG00000211892.4.IGHG4	55.311071	-4.0385483	1.1007085	-3.669044	0.0002435	0.2342615	4.724274	4.329657	7.134466	5.804448	7.542032	4.680731	5.641965	8.197161	7.810251	5.531252	6.292706	6.899070	6.237144	4.873098	4.949491	7.290447	5.678375	6.277896	4.819604	4.329657
ENSG00000286647.1.AC008459.1	22.973302	2.7680012	0.7616661	3.634140	0.0002789	0.2542481	6.749609	5.204701	5.336118	7.280025	6.419102	5.646524	4.880711	5.331162	5.246227	5.489790	6.803685	4.792124	5.010736	5.208687	4.914533	4.837700	5.117042	5.999041	5.235711	5.315586
ENSG00000254415.3.SIGLEC14	28.581734	-2.1844359	0.6074907	-3.595834	0.0003234	0.2602930	5.545167	5.130441	6.521276	4.739816	7.202307	6.053922	6.062388	5.939228	5.654565	5.844182	5.181894	6.190270	5.674266	5.324392	5.526768	5.951872	5.852374	6.374027	6.484659	4.993925

dge1 <- dge
write.table(dge1,file="rc1.tsv",quote=FALSE,sep='\t')

# mitch
m1 <- mitch_import(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 = 17320

## Note: no. genes in output = 17294

## Note: estimated proportion of input genes in output = 0.998

mres1 <- mitch_calc(m1, genesets, priority="effect")

## Note: Enrichments with large effect sizes may not be
##             statistically significant.

head(mres1$enrichment_result,20) %>%
  kbl(caption = "Top gene pathway differences between OA (ctrl) and Rotator cuff arthropathy (case)") %>%
  kable_paper("hover", full_width = F)

Top gene pathway differences between OA (ctrl) and Rotator cuff arthropathy (case)
	set	setSize	pANOVA	s.dist	p.adjustANOVA
1107	SARS-CoV-1 modulates host translation machinery	36	0.00e+00	0.7525882	0.0000000
859	Peptide chain elongation	87	0.00e+00	0.7319562	0.0000000
373	Eukaryotic Translation Elongation	92	0.00e+00	0.7227762	0.0000000
202	Classical antibody-mediated complement activation	13	7.30e-06	-0.7183568	0.0002075
1435	Viral mRNA Translation	87	0.00e+00	0.7165976	0.0000000
1153	Selenocysteine synthesis	91	0.00e+00	0.6979264	0.0000000
418	Formation of a pool of free 40S subunits	99	0.00e+00	0.6967911	0.0000000
375	Eukaryotic Translation Termination	91	0.00e+00	0.6736475	0.0000000
789	Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)	93	0.00e+00	0.6644531	0.0000000
627	L13a-mediated translational silencing of Ceruloplasmin expression	109	0.00e+00	0.6547640	0.0000000
426	Formation of the ternary complex, and subsequently, the 43S complex	51	0.00e+00	0.6478002	0.0000000
1091	Response of EIF2AK4 (GCN2) to amino acid deficiency	99	0.00e+00	0.6435562	0.0000000
464	GTP hydrolysis and joining of the 60S ribosomal subunit	110	0.00e+00	0.6427755	0.0000000
385	FCGR activation	20	7.00e-07	-0.6394929	0.0000259
230	Creation of C4 and C2 activators	16	1.28e-05	-0.6300064	0.0003294
154	Cap-dependent Translation Initiation	117	0.00e+00	0.6027057	0.0000000
374	Eukaryotic Translation Initiation	117	0.00e+00	0.6027057	0.0000000
1113	SARS-CoV-2 modulates host translation machinery	49	0.00e+00	0.5997420	0.0000000
377	Expression and translocation of olfactory receptors	22	1.30e-06	0.5952145	0.0000452
1385	Translation initiation complex formation	58	0.00e+00	0.5895779	0.0000000

m1top <- subset(mres1$enrichment_result,p.adjustANOVA<0.05)
m1up <- subset(m1top,s.dist>0)$set
m1dn <- subset(m1top,s.dist<0)$set

if (! file.exists("mitchres1.html") ) {
  mitch_report(mres1,outfile="mitchres1.html",overwrite=FALSE)
}

Primary OA vs Rotator cuff repair

ss2 <- rbind(caps_oa,caps_rcr)
ss2 <- ss2[order(rownames(ss2)),]

x2 <- xcaps[,colnames(xcaps) %in% rownames(ss2)]
x2 <- x2[,order(colnames(x2)),]

colnames(x2) == rownames(ss2)

##  [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
## [16] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
## [31] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE

x2f <- x2[which(rowMeans(x2)>10),]
dim(x2)

## [1] 60651    42

dim(x2f)

## [1] 16705    42

dds <- DESeqDataSetFromMatrix(countData = x2f , colData = ss2, design = ~ Age +Sex + group )

## 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),])
head(dge,20) %>%
  kbl(caption = "Top gene expression differences between OA (ctrl) and Rotator cuff repair (case)") %>%
  kable_paper("hover", full_width = F)

Top gene expression differences between OA (ctrl) and Rotator cuff repair (case)
	baseMean	log2FoldChange	lfcSE	stat	1.1_S41	10.1_S50	11.1_S51	11C_S36	12.1_S52	12C_S37	13.1_S53	14.1_S54	14C_S39	15.1_S55	15C_S40	16.1_S56	16C_S41	17.1_S57	17C_S42	18.1_S58	18C_S43	19.1_S59	19C_S44	2.1_S42	20.1_S60	20C_S45	21.1_S61	22.1_S62	23.1_S63	24.1_S64	25.1_S65	26.1_S66	3.1_S43	4.1_S44	4001.41C	4002.42C	4004.44C	4005.45C	4006.46C	5.1_S45	6.1_S46	7.1_S47	7C_S32	8.1_S48	8C_S33	9.1_S49
ENSG00000244734.4.HBB	26408.94502	-8.2936234	0.6585287	-12.594171	7.730444	6.927829	11.621816	13.489814	7.219295	15.120179	7.548888	7.805550	18.527603	8.247311	7.144760	9.488205	18.464709	7.970497	13.440368	9.529654	13.383956	11.157503	14.585356	9.397367	8.401227	16.734362	9.037870	9.582985	7.858982	9.351362	8.654512	8.972151	8.134942	7.156709	10.927358	13.849817	15.250202	14.414646	11.926372	7.253820	8.745659	8.046384	14.991733	8.106168	15.297268	8.475798
ENSG00000206172.8.HBA1	10920.84090	-8.4039577	0.6789623	-12.377649	6.562396	6.509066	10.169887	12.471916	6.065446	13.898980	5.689224	6.627469	17.330149	7.628291	6.185332	8.356115	16.984877	6.615640	12.133089	8.709734	12.577189	10.210002	13.479130	8.280685	7.585887	15.762876	7.970713	8.295039	6.520014	8.213778	7.349010	7.716573	7.186652	6.436943	9.957020	12.254096	13.845039	13.226695	10.534764	6.141612	6.466155	6.464266	13.763317	7.413908	13.897577	7.286260
ENSG00000188536.13.HBA2	26063.87177	-8.2897130	0.6758775	-12.265112	6.928521	6.430872	11.280813	13.588013	7.293541	14.934003	7.274720	7.243443	18.513988	8.475975	6.810039	9.522945	18.256560	7.814664	13.475089	10.111754	13.531072	11.141565	14.607189	9.371972	8.672923	16.697968	9.060085	9.225316	7.435567	8.970028	7.941837	8.342638	7.719731	7.246738	11.338812	14.312059	16.160145	15.156067	12.091832	6.891973	7.900007	6.985447	14.770785	8.350251	15.005138	8.516101
ENSG00000174938.14.SEZ6L2	45.93974	-3.3486520	0.2747392	-12.188478	5.247585	4.996285	5.445648	8.170560	5.217043	7.528467	5.445101	5.246118	6.580348	5.559294	7.495945	5.551482	6.622243	5.172915	7.095451	5.491022	7.629733	4.998798	6.291728	5.200387	5.355622	6.391939	5.122106	4.891005	4.895681	5.169769	5.092211	5.270740	5.412091	5.180123	6.487020	7.107261	6.778602	7.709299	7.188658	4.998052	5.652699	5.665120	7.350030	5.106497	7.267883	5.351438
ENSG00000116741.8.RGS2	365.02624	-3.1699720	0.3208617	-9.879558	6.648952	6.546451	7.255122	10.494124	6.577132	9.325546	7.348473	7.123032	10.043022	6.761161	8.925678	7.125627	9.504432	7.801936	9.233823	7.406640	8.064719	6.922921	7.904148	6.614388	6.310196	9.073214	6.823259	6.557512	7.181198	8.785071	7.529591	7.353566	6.898714	7.284946	8.193371	11.275590	9.950858	9.866536	9.541740	6.863090	6.757606	6.800694	10.057074	6.608250	9.699622	7.303370
ENSG00000004939.15.SLC4A1	40.21098	-5.7550054	0.6028427	-9.546446	4.817946	5.158806	4.868790	6.262094	5.074732	6.628867	4.427155	4.427155	8.542511	5.399125	5.611020	5.115879	7.222594	4.734430	6.009051	5.072058	6.121939	5.293024	8.367161	4.427155	5.134091	8.755695	4.427155	4.891005	4.999739	5.227839	4.849992	4.965195	4.705232	4.737455	5.157617	5.643287	7.204590	5.983029	5.609324	4.758190	4.427155	4.745582	7.208637	4.859173	6.211422	5.017641
ENSG00000163464.8.CXCR1	37.73675	-5.9810773	0.6323897	-9.457898	4.817946	4.892842	5.810236	5.362008	4.752975	6.838799	5.292408	4.765228	9.456941	4.919983	5.147172	5.025001	7.019435	4.427155	5.855005	4.427155	5.276607	4.998798	6.128580	5.082847	4.427155	6.988656	5.187004	5.495120	4.895681	4.955127	4.427155	5.027846	5.156235	4.737455	5.766331	7.253262	7.289637	5.670219	5.160048	4.427155	5.419887	4.745582	7.440131	4.733206	6.986560	5.017641
ENSG00000012223.13.LTF	55.59289	-6.4307966	0.6816492	-9.434173	4.817946	4.996285	4.967005	5.005815	4.886966	5.594417	4.818730	4.765228	6.077658	4.776480	5.275677	5.115879	6.173486	4.957388	6.219524	5.004920	6.871795	4.894908	8.563405	5.144224	4.427155	10.145293	4.740344	4.427155	4.427155	4.733110	4.849992	4.697342	4.705232	4.865148	5.654293	7.092275	8.731560	6.649414	5.875397	5.229426	4.902271	4.427155	6.465158	4.955292	5.422956	5.017641
ENSG00000163221.9.S100A12	27.02550	-7.3871268	0.7928509	-9.317170	4.703907	4.427155	4.967005	4.427155	4.427155	5.822131	5.101317	4.427155	7.638609	4.427155	4.885346	4.427155	6.922201	4.427155	5.162588	4.427155	5.783880	4.894908	7.230692	4.427155	4.427155	8.644925	4.869211	4.891005	4.427155	4.427155	4.726679	4.697342	4.705232	4.427155	5.267719	6.698915	7.150141	5.330895	5.187102	4.758190	5.007758	4.745582	7.478384	4.733206	5.872461	4.427155
ENSG00000144655.15.CSRNP1	193.09305	-2.7682463	0.2978173	-9.295115	6.441892	7.524271	6.899723	7.132172	6.726200	8.239647	7.114279	6.698243	7.462042	6.143683	8.145652	6.518744	8.431894	7.196215	8.188084	7.159275	7.511754	6.865719	7.656737	6.586109	6.257383	9.936302	6.555946	7.585161	6.038769	6.803777	7.008694	6.695462	6.947906	6.736367	8.563527	10.436840	8.417844	7.473084	8.867342	6.415960	6.724515	6.586263	9.745461	6.562131	8.437344	7.021409
ENSG00000158578.21.ALAS2	31.20546	-7.0046574	0.7555988	-9.270340	4.703907	4.996285	5.049330	5.689147	4.427155	6.713580	4.427155	4.765228	8.515193	4.427155	4.751823	4.427155	7.110202	4.427155	5.786817	4.717481	5.998500	4.998798	7.347827	4.843978	4.427155	8.555845	4.427155	4.427155	4.427155	5.106287	5.092211	4.697342	4.819812	4.427155	4.892076	5.766749	7.215984	6.635511	5.433906	4.427155	4.763868	4.427155	6.317240	4.859173	5.777364	4.723939
ENSG00000134686.18.PHC2	426.88885	-0.9603702	0.1050012	-9.146279	8.759710	8.471190	8.527033	9.318784	8.747636	9.270438	8.401966	8.200825	9.733041	8.253346	9.308842	8.223066	9.448991	9.028319	9.233823	8.255082	9.159555	8.758920	8.777655	8.502758	8.509892	9.347932	8.489057	8.881423	8.071772	8.461446	8.350425	8.567267	8.653419	8.465265	9.099309	9.305928	9.080320	9.534330	9.617479	8.286821	8.676592	8.446972	9.321597	8.367407	9.276618	8.449548
ENSG00000148344.11.PTGES	339.24592	-3.1352365	0.3497212	-8.964959	6.985552	6.162090	6.195403	10.906434	6.505003	7.988305	6.970920	7.693051	9.372142	6.846144	8.162372	7.310909	6.780627	6.365922	8.979636	6.868730	9.312711	6.288545	8.311401	6.721788	6.433227	7.842448	6.588472	6.319211	6.594012	7.272704	6.896973	7.783169	6.816078	7.146334	8.510842	10.501442	9.697151	10.962891	10.104212	6.588534	6.968864	6.057307	10.214713	7.336619	10.058311	6.624012
ENSG00000118785.14.SPP1	4063.95258	-6.4281549	0.7428395	-8.653491	9.269593	6.234961	7.394699	15.959092	6.117231	11.462537	7.536383	7.396175	11.604187	5.607052	14.738692	8.223066	14.103103	9.666102	10.754848	5.657199	9.188354	6.169030	8.358723	6.571736	6.144396	6.439838	6.218621	7.738627	5.231767	6.412461	6.084206	8.034710	7.094344	6.505966	7.210158	14.906413	12.316603	10.737821	12.014976	5.548010	8.741687	6.882986	11.126297	5.546180	12.693283	4.939413
ENSG00000163736.4.PPBP	15.23241	-7.1217351	0.8478957	-8.399306	4.427155	4.427155	4.967005	4.762731	4.427155	5.550844	4.427155	4.765228	7.625787	4.427155	4.427155	4.773961	6.046993	4.860894	4.758892	4.427155	6.092274	5.085823	5.276250	4.843978	4.929509	6.236200	4.740344	4.755850	4.427155	5.035692	4.427155	4.427155	4.427155	4.427155	5.025665	5.379899	6.719969	5.478311	5.160048	4.427155	4.427155	4.745582	6.930379	4.733206	7.601323	4.427155
ENSG00000159339.13.PADI4	20.49196	-5.1205161	0.6125957	-8.358719	4.817946	4.427155	4.967005	5.093873	4.752975	5.888267	5.101317	4.427155	7.137567	5.029303	4.427155	5.195396	6.341445	4.734430	5.635506	4.717481	6.179146	4.758627	6.610728	4.722404	4.427155	8.046011	5.049919	5.343381	4.895681	5.035692	4.944108	4.697342	4.427155	4.737455	5.246997	6.526815	6.926582	5.670219	4.967587	4.758190	4.902271	4.745582	7.138168	4.859173	5.987701	5.147890
ENSG00000008516.18.MMP25	88.10362	-4.1863176	0.5034849	-8.314683	5.477317	5.588019	6.415328	6.162758	5.217043	6.611249	6.012583	5.176392	10.906505	5.455767	5.650282	5.598944	7.992034	5.511446	7.155895	5.716505	5.743593	5.455745	6.418719	5.390120	5.628850	8.144642	5.122106	6.051614	5.551206	5.379120	5.485176	5.516714	5.770625	5.437514	6.240125	7.235268	7.623060	6.158545	5.862940	5.349721	6.059488	5.367636	8.007111	5.281869	7.257665	5.513717
ENSG00000162747.12.FCGR3B	94.39565	-4.6748316	0.5626624	-8.308414	5.572778	5.499201	6.195403	5.689147	4.989133	7.425087	6.090110	5.737081	10.142048	4.427155	5.482540	5.392333	9.076977	5.038288	6.195151	5.415153	6.804919	5.404939	7.321659	5.737060	4.427155	7.932154	5.981465	5.906534	4.759177	4.955127	5.154429	5.782721	5.547138	4.865148	6.293551	8.508504	8.623728	6.137979	6.089169	5.403692	5.939819	5.549107	8.706273	5.169998	8.387482	5.394965
ENSG00000187764.12.SEMA4D	99.58780	-1.6020488	0.1976566	-8.105211	6.928521	6.669447	6.679655	8.651039	6.559472	7.214933	6.872996	6.297946	8.812975	6.878686	7.888270	6.539377	7.754660	6.488507	7.571844	6.217129	6.981404	6.517035	6.984274	6.316812	6.114415	7.574452	6.572311	6.443918	6.291278	6.376826	6.189422	6.749392	6.633691	6.908060	6.747566	7.903067	7.520488	7.395306	7.014934	6.436321	6.982762	6.619114	7.774980	6.608250	7.679326	6.581228
ENSG00000105290.13.APLP1	28.07845	-3.1719254	0.3915249	-8.101465	5.201790	4.996285	5.608103	7.389846	5.217043	6.538304	4.818730	4.765228	6.464660	5.399125	6.480037	5.728949	7.222594	5.550457	6.065282	5.286830	7.054618	5.592948	6.106545	5.301029	5.215616	7.594661	5.049919	4.891005	5.406508	5.506978	5.264075	5.027846	5.103157	5.115789	5.823743	5.965523	6.365312	6.830126	5.875397	5.084966	4.763868	4.876575	6.615620	5.840483	5.959977	4.939413

dge2 <- dge
write.table(dge2,file="rc2.tsv",quote=FALSE,sep='\t')

# mitch
m2 <- mitch_import(dge2, 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 = 16705

## Note: no. genes in output = 16680

## Note: estimated proportion of input genes in output = 0.999

mres2 <- mitch_calc(m2, genesets, priority="effect")

## Note: Enrichments with large effect sizes may not be
##             statistically significant.

head(mres2$enrichment_result,20) %>%
  kbl(caption = "Top gene pathway differences between OA (ctrl) and Rotator cuff repair (case)") %>%
  kable_paper("hover", full_width = F)

Top gene pathway differences between OA (ctrl) and Rotator cuff repair (case)
	set	setSize	pANOVA	s.dist	p.adjustANOVA
698	Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane	13	0.0000156	-0.6918923	0.0001098
425	Formation of tubulin folding intermediates by CCT/TriC	21	0.0000002	-0.6558874	0.0000021
1394	Transport of connexons to the plasma membrane	14	0.0000442	-0.6303595	0.0002944
405	Folding of actin by CCT/TriC	10	0.0008713	-0.6079304	0.0043746
898	Prefoldin mediated transfer of substrate to CCT/TriC	25	0.0000002	-0.5974590	0.0000024
225	Cooperation of Prefoldin and TriC/CCT in actin and tubulin folding	28	0.0000001	-0.5883635	0.0000008
370	Eukaryotic Translation Elongation	92	0.0000000	-0.5802269	0.0000000
616	Josephin domain DUBs	10	0.0016906	-0.5733773	0.0078949
856	Peptide chain elongation	87	0.0000000	-0.5733431	0.0000000
1309	TP53 Regulates Transcription of Death Receptors and Ligands	10	0.0018380	-0.5688902	0.0085292
482	Gluconeogenesis	27	0.0000004	-0.5659819	0.0000034
1424	Viral mRNA Translation	87	0.0000000	-0.5654933	0.0000000
364	Erythrocytes take up carbon dioxide and release oxygen	10	0.0020114	-0.5640192	0.0091320
809	O2/CO2 exchange in erythrocytes	10	0.0020114	-0.5640192	0.0091320
619	Keratan sulfate biosynthesis	26	0.0000006	-0.5639209	0.0000060
372	Eukaryotic Translation Termination	91	0.0000000	-0.5528680	0.0000000
1126	STAT3 nuclear events downstream of ALK signaling	10	0.0028063	-0.5456989	0.0122132
1100	SARS-CoV-1 modulates host translation machinery	36	0.0000000	-0.5456821	0.0000002
415	Formation of a pool of free 40S subunits	99	0.0000000	-0.5421728	0.0000000
786	Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)	93	0.0000000	-0.5394904	0.0000000

m2top <- subset(mres2$enrichment_result,p.adjustANOVA<0.05)
m2up <- subset(m2top,s.dist>0)$set
m2dn <- subset(m2top,s.dist<0)$set

if (! file.exists("mitchres2.html") ) {
  mitch_report(mres2,outfile="mitchres2.html",overwrite=FALSE)
}

Rotator cuff repair vs Rotator cuff arthropathy

ss3 <- rbind(caps_rcr,caps_rca)
ss3 <- ss3[order(rownames(ss3)),]

x3 <- xcaps[,colnames(xcaps) %in% rownames(ss3)]
x3 <- x3[,order(colnames(x3)),]

colnames(x3) == rownames(ss3)

##  [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
## [16] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE

x3f <- x3[which(rowMeans(x3)>10),]
dim(x3)

## [1] 60651    30

dim(x3f)

## [1] 16458    30

ss3$group <- factor(ss3$group,levels=c("rcr","rca"))
dds <- DESeqDataSetFromMatrix(countData = x3f , colData = ss3, design = ~ Age +Sex + group )

## 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),])
head(dge,20) %>%
  kbl(caption = "Top gene expression differences between Rotator cuff repair (ctrl) and Rotator cuff arthropathy (case)") %>%
  kable_paper("hover", full_width = F)

Top gene expression differences between Rotator cuff repair (ctrl) and Rotator cuff arthropathy (case)
	baseMean	log2FoldChange	lfcSE	stat	padj	1.1_S41	10.1_S50	10C_S35	11.1_S51	12.1_S52	13.1_S53	13C_S38	14.1_S54	15.1_S55	16.1_S56	17.1_S57	18.1_S58	19.1_S59	2.1_S42	20.1_S60	21.1_S61	22.1_S62	23.1_S63	24.1_S64	25.1_S65	26.1_S66	3.1_S43	4.1_S44	4003.43C	5.1_S45	6.1_S46	7.1_S47	8.1_S48	9.1_S49	9C_S34
ENSG00000244734.4.HBB	8683.63048	8.609168	0.8354719	10.304558	0.0e+00	7.649190	6.801459	16.909440	11.574409	7.111538	7.457752	16.584890	7.718199	8.152491	9.422418	7.893024	9.476276	11.102239	9.331990	8.319315	8.978806	9.528001	7.774612	9.290159	8.582883	8.912174	8.062289	7.048427	12.071313	7.151403	8.685301	7.969273	8.028078	8.403013	14.431621
ENSG00000206172.8.HBA1	4363.08548	9.041692	0.9406335	9.612343	0.0e+00	6.431697	6.362347	15.795920	10.116895	5.897242	5.496608	15.742367	6.493754	7.518716	8.274806	6.485610	8.646111	10.150719	8.199086	7.484287	7.891734	8.221812	6.381651	8.135122	7.244827	7.630544	7.084279	6.293478	10.296412	5.981368	6.328613	6.324570	7.315836	7.181463	13.648784
ENSG00000188536.13.HBA2	8493.63274	8.629791	0.9383985	9.196297	0.0e+00	6.816730	6.279880	16.649254	11.232542	7.188595	7.173845	16.785358	7.137642	8.385340	9.457476	7.732990	10.062927	11.086252	9.306342	8.595658	9.001308	9.166686	7.338187	8.904327	7.855614	8.272119	7.636062	7.142003	12.131226	6.774111	7.821884	6.872454	8.277438	8.444045	14.510028
ENSG00000099860.9.GADD45B	389.63184	2.390950	0.3127038	7.646054	0.0e+00	7.852849	7.689409	11.375782	7.670646	8.033963	8.098846	9.906551	8.249055	7.602748	8.257815	8.603479	8.365735	8.256330	8.030420	7.686036	8.239017	8.437255	7.619060	7.600653	8.339220	8.088512	8.233730	8.364592	9.315684	8.553738	7.955316	7.812972	7.625244	7.994185	10.456176
ENSG00000012223.13.LTF	31.06759	5.951529	0.8234985	7.227128	0.0e+00	4.549438	4.740650	8.936273	4.710875	4.623201	4.549554	8.394691	4.490344	4.499948	4.871200	4.701609	4.753262	4.630957	4.902350	4.120228	4.463673	4.120228	4.120228	4.455033	4.582562	4.416542	4.425475	4.599786	5.399230	4.997887	4.641540	4.120228	4.698419	4.765918	7.095788
ENSG00000067048.17.DDX3Y	306.68759	8.531180	1.1880304	7.180944	0.0e+00	8.442575	8.745731	5.003288	9.192367	8.798102	4.120228	8.754476	9.084546	8.406157	8.789677	9.043086	8.752548	4.120228	9.128602	8.890513	9.139576	4.480416	9.037174	4.120228	4.120228	9.022616	8.983458	8.820268	4.120228	4.120228	8.325426	4.120228	9.014919	8.783129	8.983150
ENSG00000144655.15.CSRNP1	169.83167	3.493242	0.4892156	7.140497	0.0e+00	6.304200	7.420191	10.891134	6.779583	6.596652	7.006976	8.783124	6.568197	5.969734	6.374060	7.093526	7.053907	6.739148	6.445900	6.096775	6.421467	7.493471	5.870445	6.677891	6.891128	6.568448	6.835189	6.609085	7.344177	6.272929	6.601221	6.453439	6.426150	6.905975	9.769830
ENSG00000116985.12.BMP8B	132.15992	4.022540	0.5678857	7.083361	0.0e+00	5.731250	5.912744	9.464536	5.939761	7.017933	5.496608	9.565882	6.769727	6.215946	6.519271	6.578126	5.698272	6.290319	5.844237	6.509661	6.312833	6.301788	6.114997	6.372878	6.207917	6.067865	5.530099	5.613748	6.121467	6.294487	6.842785	6.159881	6.721318	5.780247	10.436216
ENSG00000163884.4.KLF15	142.42969	5.145061	0.7436502	6.918657	0.0e+00	5.405136	6.742483	10.251302	6.433930	5.868660	5.066712	9.648558	6.785251	6.288515	5.965115	6.141010	6.001914	6.450924	5.819858	5.944942	6.274531	5.995950	5.562988	5.686114	6.006808	5.310099	5.309533	5.677306	4.571587	5.866878	5.955212	5.430417	5.717653	6.629722	10.505859
ENSG00000071859.15.FAM50A	966.65910	2.980866	0.4484734	6.646695	0.0e+00	8.751667	9.221880	11.367731	8.917189	9.216197	8.688618	9.427706	9.196419	8.967753	9.128144	9.837886	9.176495	9.309319	9.023515	9.205086	8.912081	8.825339	8.932660	9.499784	9.349098	8.790144	8.838106	9.499406	9.590915	9.153879	8.759895	8.667734	9.250155	9.425933	13.475427
ENSG00000120875.9.DUSP4	24.03426	3.522494	0.5309708	6.634063	0.0e+00	5.821983	5.285488	6.566377	5.323207	4.909647	5.553304	7.904625	4.854540	4.655706	4.957550	5.696230	5.008572	4.921642	5.511224	5.259659	5.234125	5.762073	5.244778	5.207250	5.314314	5.241436	5.663778	5.546362	6.303859	4.997887	4.853571	5.091812	5.160267	5.176212	6.942869
ENSG00000229391.7.HLA.DRB6	70.55897	-4.158651	0.6456217	-6.441313	2.0e-07	6.445134	6.898948	4.808428	6.831666	6.383208	6.711693	4.120228	7.338135	7.732616	6.650291	5.754568	6.796550	7.052097	6.368465	6.966003	6.521883	7.439626	6.139445	5.339186	6.460892	6.792142	7.197794	7.048427	4.532538	6.875024	7.324586	7.019077	5.717653	6.916813	5.220494
ENSG00000167978.17.SRRM2	5450.17762	-1.114458	0.1770004	-6.296357	4.0e-07	12.644032	12.538822	11.187373	12.187812	12.802738	12.642544	11.158574	12.576434	12.549859	12.602248	12.505846	12.074802	12.358340	12.277562	11.885264	12.701578	12.492847	12.550421	12.289144	12.640733	12.632503	12.796057	12.384621	11.376923	12.439713	12.687976	12.905730	12.451482	12.644990	11.893257
ENSG00000158578.21.ALAS2	26.36758	7.216130	1.1574460	6.234529	5.0e-07	4.424283	4.740650	9.057838	4.800696	4.120228	4.120228	7.860327	4.490344	4.120228	4.120228	4.120228	4.438644	4.744139	4.575446	4.120228	4.120228	4.120228	4.120228	4.862348	4.846676	4.416542	4.551115	4.120228	4.956341	4.120228	4.489848	4.120228	4.593362	4.445087	6.464160
ENSG00000183878.15.UTY	59.87221	5.419066	0.8884171	6.099687	1.2e-06	6.722063	7.014970	5.291155	7.087578	6.877983	4.120228	6.614624	6.945380	6.855196	6.909532	6.930683	6.936320	4.120228	6.995008	6.873356	7.082489	4.120228	6.960983	4.120228	4.447844	6.782281	7.075807	6.468837	4.120228	4.120228	6.653078	4.120228	6.847907	6.642968	6.834842
ENSG00000153531.13.ADPRHL1	33.13265	3.481644	0.5818089	5.984171	2.2e-06	5.436400	5.509763	6.648538	5.484666	5.746984	4.725188	8.787843	5.207696	5.446126	5.342773	5.962889	5.462094	5.703222	5.256067	5.425424	5.184563	5.426365	5.562988	5.560346	5.314314	5.404853	5.236440	5.066702	5.300304	5.805306	5.584693	5.299664	5.160267	5.381830	7.043081
ENSG00000163221.9.S100A12	16.29996	7.139573	1.1965427	5.966835	2.3e-06	4.424283	4.120228	8.399572	4.710875	4.120228	4.858508	6.909092	4.120228	4.120228	4.120228	4.120228	4.120228	4.630957	4.120228	4.120228	4.604800	4.628305	4.120228	4.120228	4.447844	4.416542	4.425475	4.120228	4.729332	4.483124	4.757000	4.469410	4.455530	4.120228	6.676193
ENSG00000072310.17.SREBF1	684.59769	-1.181623	0.1993427	-5.927593	2.8e-06	9.939430	9.794358	8.794763	9.223640	9.769040	9.611393	8.100001	9.227244	9.702052	9.824583	9.375230	9.340813	9.224155	9.272098	9.037312	9.570255	9.572061	9.469366	9.488485	9.521757	9.540719	9.695443	9.537574	9.019595	9.766011	10.108805	9.858249	9.448417	9.714636	8.538025
ENSG00000203865.11.ATP1A1.AS1	57.51622	1.563173	0.2676147	5.841134	4.4e-06	6.211749	6.439959	7.116870	6.654609	6.439850	5.707819	7.209856	5.957400	6.334745	6.374060	6.706010	6.157274	6.373062	6.023439	6.401084	6.421467	7.015925	6.038691	6.389900	6.297771	6.801933	6.518075	6.090854	6.544122	6.086163	5.895872	6.362689	6.172034	6.397882	7.350490
ENSG00000173530.6.TNFRSF10D	88.78480	1.852497	0.3175053	5.834538	4.4e-06	6.886102	6.815815	7.973565	6.930275	6.476314	6.733478	8.801910	6.512755	6.582645	6.458964	7.182825	6.666051	6.676637	6.574880	6.774041	6.784834	6.459512	6.653526	6.471880	6.606215	6.497112	6.865183	6.681137	6.624155	6.510917	6.284656	6.554768	6.721318	6.264799	7.693592

dge3 <- dge
write.table(dge3,file="rc3.tsv",quote=FALSE,sep='\t')

# mitch
m3 <- mitch_import(dge3, 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 = 16458

## Note: no. genes in output = 16432

## Note: estimated proportion of input genes in output = 0.998

mres3 <- mitch_calc(m3, genesets, priority="effect")

## Note: Enrichments with large effect sizes may not be
##             statistically significant.

head(mres3$enrichment_result,20) %>%
  kbl(caption = "Top gene pathway differences between Rotator cuff repair (ctrl) and Rotator cuff arthropathy (case)") %>%
  kable_paper("hover", full_width = F)

Top gene pathway differences between Rotator cuff repair (ctrl) and Rotator cuff arthropathy (case)
	set	setSize	pANOVA	s.dist	p.adjustANOVA
370	Eukaryotic Translation Elongation	91	0.0000000	0.7187456	0.0000000
850	Peptide chain elongation	87	0.0000000	0.7128821	0.0000000
1417	Viral mRNA Translation	87	0.0000000	0.7054757	0.0000000
414	Formation of a pool of free 40S subunits	99	0.0000000	0.6846973	0.0000000
1092	SARS-CoV-1 modulates host translation machinery	36	0.0000000	0.6824022	0.0000000
782	Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)	93	0.0000000	0.6767218	0.0000000
372	Eukaryotic Translation Termination	91	0.0000000	0.6730156	0.0000000
424	Formation of tubulin folding intermediates by CCT/TriC	20	0.0000002	0.6700768	0.0000034
1138	Selenocysteine synthesis	91	0.0000000	0.6671045	0.0000000
623	L13a-mediated translational silencing of Ceruloplasmin expression	109	0.0000000	0.6666942	0.0000000
461	GTP hydrolysis and joining of the 60S ribosomal subunit	110	0.0000000	0.6582827	0.0000000
404	Folding of actin by CCT/TriC	10	0.0003835	0.6484716	0.0026738
1117	SRP-dependent cotranslational protein targeting to membrane	110	0.0000000	0.6451939	0.0000000
891	Prefoldin mediated transfer of substrate to CCT/TriC	24	0.0000001	0.6362496	0.0000014
423	Formation of the ternary complex, and subsequently, the 43S complex	51	0.0000000	0.6352182	0.0000000
1078	Response of EIF2AK4 (GCN2) to amino acid deficiency	99	0.0000000	0.6332368	0.0000000
153	Cap-dependent Translation Initiation	117	0.0000000	0.6310039	0.0000000
371	Eukaryotic Translation Initiation	117	0.0000000	0.6310039	0.0000000
695	Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane	12	0.0001573	0.6300041	0.0012061
226	Cooperation of Prefoldin and TriC/CCT in actin and tubulin folding	27	0.0000000	0.6285550	0.0000004

m3top <- subset(mres3$enrichment_result,p.adjustANOVA<0.05)
m3up <- subset(m3top,s.dist>0)$set
m3dn <- subset(m3top,s.dist<0)$set

if (! file.exists("mitchres1.html") ) {
  mitch_report(mres3,outfile="mitchres3.html",overwrite=FALSE)
}

Session information

For reproducibility.

sessionInfo()

## R version 4.3.2 (2023-10-31)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 22.04.4 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_1.3.3               GGally_2.2.0               
##  [3] beeswarm_0.4.0              gtools_3.9.5               
##  [5] echarts4r_0.4.5             kableExtra_1.3.4           
##  [7] topconfects_1.18.0          limma_3.58.1               
##  [9] eulerr_7.0.0                mitch_1.14.0               
## [11] MASS_7.3-60                 fgsea_1.28.0               
## [13] gplots_3.1.3                DESeq2_1.42.0              
## [15] SummarizedExperiment_1.32.0 Biobase_2.62.0             
## [17] MatrixGenerics_1.14.0       matrixStats_1.2.0          
## [19] GenomicRanges_1.54.1        GenomeInfoDb_1.38.5        
## [21] IRanges_2.36.0              S4Vectors_0.40.2           
## [23] BiocGenerics_0.48.1         reshape2_1.4.4             
## [25] lubridate_1.9.3             forcats_1.0.0              
## [27] stringr_1.5.1               dplyr_1.1.4                
## [29] purrr_1.0.2                 readr_2.1.4                
## [31] tidyr_1.3.0                 tibble_3.2.1               
## [33] ggplot2_3.4.4               tidyverse_2.0.0            
## [35] zoo_1.8-12                  R.utils_2.12.3             
## [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_1.1.2            
##  [4] magrittr_2.0.3          compiler_4.3.2          systemfonts_1.0.5      
##  [7] vctrs_0.6.5             rvest_1.0.3             pkgconfig_2.0.3        
## [10] crayon_1.5.2            fastmap_1.1.1           XVector_0.42.0         
## [13] ellipsis_0.3.2          caTools_1.18.2          utf8_1.2.4             
## [16] promises_1.2.1          rmarkdown_2.25          tzdb_0.4.0             
## [19] xfun_0.41               zlibbioc_1.48.0         cachem_1.0.8           
## [22] jsonlite_1.8.8          highr_0.10              later_1.3.2            
## [25] DelayedArray_0.28.0     BiocParallel_1.36.0     parallel_4.3.2         
## [28] R6_2.5.1                bslib_0.6.1             stringi_1.8.3          
## [31] RColorBrewer_1.1-3      jquerylib_0.1.4         assertthat_0.2.1       
## [34] Rcpp_1.0.11             knitr_1.45              httpuv_1.6.13          
## [37] Matrix_1.6-4            timechange_0.2.0        tidyselect_1.2.0       
## [40] rstudioapi_0.15.0       abind_1.4-5             yaml_2.3.8             
## [43] codetools_0.2-19        lattice_0.22-5          plyr_1.8.9             
## [46] shiny_1.8.0             withr_2.5.2             evaluate_0.23          
## [49] ggstats_0.5.1           xml2_1.3.6              pillar_1.9.0           
## [52] KernSmooth_2.23-22      generics_0.1.3          RCurl_1.98-1.13        
## [55] hms_1.1.3               munsell_0.5.0           scales_1.3.0           
## [58] xtable_1.8-4            glue_1.6.2              tools_4.3.2            
## [61] data.table_1.14.10      webshot_0.5.5           locfit_1.5-9.8         
## [64] fastmatch_1.1-4         cowplot_1.1.2           grid_4.3.2             
## [67] colorspace_2.1-0        GenomeInfoDbData_1.2.11 cli_3.6.2              
## [70] fansi_1.0.6             viridisLite_0.4.2       S4Arrays_1.2.0         
## [73] svglite_2.1.3           gtable_0.3.4            sass_0.4.8             
## [76] digest_0.6.33           SparseArray_1.2.3       htmlwidgets_1.6.4      
## [79] htmltools_0.5.7         lifecycle_1.0.4         httr_1.4.7             
## [82] statmod_1.5.0           mime_0.12