Source: TBA
baseDir=getwd()
dataDir=paste(baseDir,"/him_chart_idats/CHART_idats",sep="")
suppressPackageStartupMessages({
library("missMethyl")
library("limma")
library("minfi")
library("IlluminaHumanMethylation450kanno.ilmn12.hg19")
library("IlluminaHumanMethylationEPICanno.ilm10b2.hg19")
library("ruv")
library("RColorBrewer")
library("matrixStats")
library("gplots")
library("FlowSorted.Blood.450k")
library("reshape2")
library("ggplot2")
library("DMRcate")
library("FlowSorted.Blood.EPIC")
library("mitch")
library("kableExtra")
library("vioplot")
library("WGCNA")
})
#source("meth_functions.R")
Load the annotation data and the Epic methylation data.
This analysis is to be conducted on Ubuntu with R4.
ann = getAnnotation(IlluminaHumanMethylationEPICanno.ilm10b2.hg19)
ann_sub = ann[,c("chr","pos","strand","Name","Islands_Name",
"Relation_to_Island","UCSC_RefGene_Name","UCSC_RefGene_Group")]
targets_gen = read.metharray.sheet(dataDir, pattern = "CHART_sample_sheet_adults.csv")
## [read.metharray.sheet] Found the following CSV files:
## [1] "/analysis/him_chart_idats/CHART_idats/CHART_sample_sheet_adults.csv"
#targets$ID = paste(targets$Sample_Group,targets_gen$Sample_Name,sep=".")
rgSet = read.metharray.exp(targets = targets_gen)
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
## Warning in readChar(con, nchars = n): truncating string with embedded nuls
sampleNames(rgSet) = targets_gen$sample_id
rgSet$Slide <- as.numeric(rgSet$Slide)
rgSet$gender_m_f <- as.character(rgSet$gender_m_f)
rgSet$Sex <- as.character(rgSet$gender_m_f)
rgSet$sample_id <- as.character(rgSet$sample_id)
targets_gen$gender_m_f <- factor(targets_gen$gender_m_f)
targets_gen$status <- factor(targets_gen$status,levels=c("control","case"))
targets_gen$birth <- factor(targets_gen$birth,levels=c("Vaginal","Elective caesarian","Emergency caesarean"))
targets_gen$gest <- as.numeric(targets_gen$gest)
## Warning: NAs introduced by coercion
targets_gen$sga2 <- factor(paste(targets_gen$sga,targets_gen$lrga),levels=c("Not small for gestational age - above 10th percentile Large for gestational age - above 90th percentile","Not small for gestational age - above 10th percentile Not large for gestational age - below 90th percentile","Small for gestational age - below 10th percentile Not large for gestational age - below 90th percentile"))
snpBetas = getSnpBeta(rgSet)
## Loading required package: IlluminaHumanMethylationEPICmanifest
d = dist(t(snpBetas))
hr = hclust(d, method = "complete", members=NULL)
plot(hr)
detP = detectionP(rgSet)
qcReport(rgSet, sampNames = targets_gen$sample_id,
pdf="qc-report_chart.pdf")
## Warning in type.convert.default(X[[i]], ...): 'as.is' should be specified by the
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## Warning in type.convert.default(X[[i]], ...): 'as.is' should be specified by the
## caller; using TRUE
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## caller; using TRUE
## Warning in type.convert.default(X[[i]], ...): 'as.is' should be specified by the
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## png
## 2
cols=brewer.pal(4,"Set1")
barplot(apply(detP,2,mean),
col=as.numeric(factor(targets_gen$Sample_Name)),
las=2,cex.names= 0.8, cex.axis=0.75,
main="Mean detection p-values of probe signals",
ylab="Mean detection p-value")
barplot(apply(detP,2,mean),
col=as.numeric(factor(targets_gen$Sample_Name)),
las=2,cex.names= 0.8, cex.axis=0.75,ylim=c(0,0.010),
main="Mean detection p-values of probe signals",
ylab="Mean detection p-value")
mset.raw = preprocessRaw(rgSet)
Using Multi-dimensional scaling (MDS) plots before filtering.
mdsPlot(mset.raw, sampGroups = targets_gen$Sample_Name,
sampNames=targets_gen$Social_interaction_on_ADOS,legendPos="bottom")
mdsPlot(mset.raw, sampGroups = targets_gen$Sex,
sampNames=targets_gen$SampleID,legendPos="bottom")
Try estimatecellcounts2.
cells <- estimateCellCounts2(rgSet, referencePlatform= "IlluminaHumanMethylationEPIC",
returnAll = TRUE)
## snapshotDate(): 2021-10-19
## see ?FlowSorted.Blood.EPIC and browseVignettes('FlowSorted.Blood.EPIC') for documentation
## downloading 1 resources
## retrieving 1 resource
## loading from cache
## [estimateCellCounts2] Combining user data with reference (flow sorted) data.
## [estimateCellCounts2] Processing user and reference data together.
## [estimateCellCounts2] Picking probes for composition estimation.
## [estimateCellCounts2] Estimating composition.
mset <- cells$normalizedData
cellCounts_new <- cells[[1]]
#plot cell type composition by sample group
a = cellCounts_new[targets_gen$Diagnosis == "0",]
b = cellCounts_new[targets_gen$Diagnosis == "1",]
c = cellCounts_new[targets_gen$Diagnosis == "2",]
age.pal <- brewer.pal(8,"Set1")
cellCounts_long <- melt(cellCounts_new, id = "celltype")
cellCounts_long$Var1 <- targets_gen[match(cellCounts_long$Var1, targets_gen$sample_id),"group_exp_new"]
colnames(cellCounts_long) <- c("ART_group","celltype","value")
head(cellCounts_long)
## ART_group celltype value
## 1 Fresh embryo CD8T 0.14527618
## 2 Fresh embryo CD8T 0.23424722
## 3 Fresh embryo CD8T 0.09020196
## 4 GIFT CD8T 0.06489822
## 5 non-ART CD8T 0.17094843
## 6 non-ART CD8T 0.13801103
detP <- detectionP(rgSet)
# exclude bad samples
sample_failed_probes <- apply(detP,2, function(x) { length(which(x>0.01)) / length(x) } )
barplot(sample_failed_probes[order(sample_failed_probes)])
bad_samples <- sample_failed_probes[sample_failed_probes>0.01]
bad_samples
## 4014_A 4051_A 4439_A 5156_A
## 0.7714432 0.9624439 0.9735132 0.9720976
bad_samples <- names(bad_samples)
good_samples <- setdiff(names(sample_failed_probes),bad_samples)
detP <- detP[,good_samples]
mset <- mset[,good_samples]
targets_gen <- targets_gen[which(targets_gen$sample_id %in% good_samples),]
# exclude bad probes
failed_prope_frac <- apply(detP,1, function(x) { length(which(x>0.01)) / length(x) } )
probes_to_keep <- names(which(failed_prope_frac<0.05))
detP <- detP[probes_to_keep,]
mset <- mset[which(rownames(mset) %in% probes_to_keep),]
dim(mset)
## [1] 864281 233
gmset <- mapToGenome(mset)
#remove SNPs
gmset_flt = dropLociWithSnps(gmset, snps = c("CpG", "SBE"))
#Removing cross-reactive probes
XURL="https://raw.githubusercontent.com/sirselim/illumina450k_filtering/master/EPIC/13059_2016_1066_MOESM1_ESM.csv"
Xreact <- read.csv(XURL)
noXreact <- !(featureNames(gmset) %in% Xreact$X)
gmset <- gmset[noXreact,]
#Removing probes on X and Y chromosomes
autosomes <- !(featureNames(gmset) %in% ann$Name[ann$chr %in% c("chrX","chrY")])
gmset_flt <- gmset[autosomes,]
#Relative log expression (RLE plot)
mvals = getM(gmset_flt)
dim(mvals)
## [1] 803094 233
medSq = apply(mvals, 1, median)
YSq = mvals - medSq
boxplot(YSq,outline=FALSE,ylim=c(-1.5,1.5),
ylab="Relative Log Methylation Value",
cols=as.character(factor(targets_gen$Social_interaction_on_ADOS,)) )
pal = brewer.pal(8, "Dark2")
mds1Sq = plotMDS(mvals, top=1000, gene.selection="common",dim.plot=c(1,2))
mds2Sq = plotMDS(mvals, top=1000, gene.selection="common",dim.plot=c(1,3))
mds3Sq = plotMDS(mvals, top=1000, gene.selection="common",dim.plot=c(2,3))
mds4Sq = plotMDS(mvals, top=1000, gene.selection="common",dim.plot=c(3,4))
plotMDS(mds1Sq, xlab="Dimension 1", ylab="Dimension 2",
col=pal[as.factor(targets_gen$group_exp_new)],
dim=c(1,2), labels=targets_gen$sample_id)
legend("bottomright",bg="white",col=pal,cex=.7,pch=1,legend=0:1)
plotMDS(mds2Sq, xlab="Dimension 1", ylab="Dimension 3",
col=pal[as.factor(targets_gen$group_exp_new)],dim=c(1,3),
labels=targets_gen$sample_id)
legend("bottomright",bg="white",col=pal,cex=.7,pch=1,legend=0:1)
plotMDS(mds3Sq, xlab="Dimension 2", ylab="Dimension 3",
col=pal[as.factor(targets_gen$group_exp_new)],dim=c(2,3),
labels=targets_gen$sample_id)
legend("bottomright",bg="white",col=pal,cex=.7,pch=1,legend=0:1)
plotMDS(mds4Sq, xlab="Dimension 3", ylab="Dimension 4",
col=pal[as.factor(targets_gen$group_exp_new)],dim=c(3,4),
labels=targets_gen$sample_id)
legend("bottomright",bg="white",col=pal,cex=.7,pch=1,legend=0:1)
fit <- prcomp(t(mvals),center = TRUE, scale = TRUE,retx=TRUE)
loadings = fit$x
plot(fit,type="lines")
nGenes = nrow(mvals)
nSamples = ncol(mvals)
datTraits = targets_gen[,c("gender_m_f","status","birth","gest","sga2")]
datTraits$gender_m_f <- as.numeric(datTraits$gender_m_f)
datTraits$status <- as.numeric(datTraits$status)
datTraits$birth <- as.numeric(datTraits$birth)
datTraits$sga2 <- as.numeric(datTraits$sga2)
moduleTraitCor = cor(loadings[,1:6], datTraits, use = "p")
moduleTraitPvalue = corPvalueStudent(moduleTraitCor, nSamples)
par(cex=0.75, mar = c(6, 8.5, 3, 3))
textMatrix = paste(signif(moduleTraitCor, 2), "\n(",
signif(moduleTraitPvalue, 1), ")", sep = "");
dim(textMatrix) = dim(moduleTraitCor)
labeledHeatmap(Matrix = t(moduleTraitCor),
xLabels = colnames(loadings)[1:ncol(t(moduleTraitCor))],
yLabels = names(datTraits), colorLabels = FALSE, colors = blueWhiteRed(6),
textMatrix = t(textMatrix), setStdMargins = FALSE, cex.text = 0.5,
cex.lab.y = 0.6, zlim = c(-1,1),
main = paste("PCA-trait relationships: Top principal components"))
pdf("pca_chart.pdf")
par(mar=c(3,8,2,2))
labeledHeatmap(Matrix = t(moduleTraitCor),
xLabels = colnames(loadings)[1:ncol(t(moduleTraitCor))],
yLabels = names(datTraits), colorLabels = FALSE, colors = blueWhiteRed(6),
textMatrix = t(textMatrix), setStdMargins = FALSE, cex.text = 0.5,
cex.lab.y = 0.6, zlim = c(-1,1),
main = paste("PCA-trait relationships: Top principal components"))
dev.off()
## png
## 2
targets_gen$art <- targets_gen$Tx_new!=".c"
art <- targets_gen$art
sex <- targets_gen$sex
design <- model.matrix(~ sex + art )
fit <- lmFit(mvals, design)
## Coefficients not estimable: artTRUE
## Warning: Partial NA coefficients for 803094 probe(s)
fit2 <- eBayes(fit)
## Warning in .ebayes(fit = fit, proportion = proportion, stdev.coef.lim =
## stdev.coef.lim, : Estimation of var.prior failed - set to default value
summary(decideTests(fit2))
## (Intercept) sexF_control sexM_case sexM_control artTRUE
## Down 262001 68 18829 11158 0
## NotSig 6938 802948 778016 767757 0
## Up 534155 78 6249 24179 0
top <- topTable(fit2,coef=ncol(design),num=Inf, sort.by = "P")
nsig <- sum(top$adj.P.Val < 0.05)
sum(top$P.Value< 0.05)
## [1] NA
output <-merge(ann_sub,top,by.x="Name",by.y="row.names")
output <- output[order(output$P.Value),]
write.csv(output, file="limma_CHART_art.csv",row.names=FALSE)
output <- subset(output,P.Value<1e-4)
head(output,30) %>% kbl() %>% kable_paper("hover", full_width = F)
Name | chr | pos | strand | Islands_Name | Relation_to_Island | UCSC_RefGene_Name | UCSC_RefGene_Group | logFC | AveExpr | t | P.Value | adj.P.Val | B |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
saveRDS(design, "CHART_art_des.rds")
saveRDS(mvals, "CHART_art_mvals.rds")
sessionInfo()
## R version 4.1.3 (2022-03-10)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.4 LTS
##
## Matrix products: default
## BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.8.so
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] parallel stats4 stats graphics grDevices utils datasets
## [8] methods base
##
## other attached packages:
## [1] IlluminaHumanMethylationEPICmanifest_0.3.0
## [2] WGCNA_1.72-1
## [3] fastcluster_1.2.3
## [4] dynamicTreeCut_1.63-1
## [5] vioplot_0.4.0
## [6] zoo_1.8-11
## [7] sm_2.2-5.7.1
## [8] kableExtra_1.3.4
## [9] mitch_1.6.0
## [10] FlowSorted.Blood.EPIC_1.12.1
## [11] ExperimentHub_2.2.1
## [12] AnnotationHub_3.2.2
## [13] BiocFileCache_2.2.1
## [14] dbplyr_2.3.2
## [15] nlme_3.1-155
## [16] quadprog_1.5-8
## [17] genefilter_1.76.0
## [18] DMRcate_2.8.5
## [19] ggplot2_3.4.1
## [20] reshape2_1.4.4
## [21] FlowSorted.Blood.450k_1.32.0
## [22] gplots_3.1.3
## [23] RColorBrewer_1.1-3
## [24] ruv_0.9.7.1
## [25] IlluminaHumanMethylationEPICanno.ilm10b2.hg19_0.6.0
## [26] limma_3.50.3
## [27] missMethyl_1.28.0
## [28] IlluminaHumanMethylationEPICanno.ilm10b4.hg19_0.6.0
## [29] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.0
## [30] minfi_1.40.0
## [31] bumphunter_1.36.0
## [32] locfit_1.5-9.7
## [33] iterators_1.0.14
## [34] foreach_1.5.2
## [35] Biostrings_2.62.0
## [36] XVector_0.34.0
## [37] SummarizedExperiment_1.24.0
## [38] Biobase_2.54.0
## [39] MatrixGenerics_1.6.0
## [40] matrixStats_0.63.0
## [41] GenomicRanges_1.46.1
## [42] GenomeInfoDb_1.30.1
## [43] IRanges_2.28.0
## [44] S4Vectors_0.32.4
## [45] BiocGenerics_0.40.0
##
## loaded via a namespace (and not attached):
## [1] rappdirs_0.3.3 rtracklayer_1.54.0
## [3] GGally_2.1.2 R.methodsS3_1.8.2
## [5] tidyr_1.3.0 bit64_4.0.5
## [7] knitr_1.37 DelayedArray_0.20.0
## [9] R.utils_2.12.2 data.table_1.14.8
## [11] rpart_4.1.16 doParallel_1.0.17
## [13] KEGGREST_1.34.0 RCurl_1.98-1.10
## [15] GEOquery_2.62.2 AnnotationFilter_1.18.0
## [17] generics_0.1.2 GenomicFeatures_1.46.5
## [19] preprocessCore_1.56.0 RSQLite_2.3.0
## [21] bit_4.0.5 tzdb_0.3.0
## [23] webshot_0.5.4 xml2_1.3.3
## [25] httpuv_1.6.9 xfun_0.37
## [27] hms_1.1.3 jquerylib_0.1.4
## [29] evaluate_0.15 promises_1.2.0.1
## [31] fansi_1.0.2 restfulr_0.0.15
## [33] scrime_1.3.5 progress_1.2.2
## [35] caTools_1.18.2 DBI_1.1.3
## [37] htmlwidgets_1.6.2 reshape_0.8.9
## [39] purrr_1.0.1 ellipsis_0.3.2
## [41] dplyr_1.1.0 backports_1.4.1
## [43] permute_0.9-7 annotate_1.72.0
## [45] biomaRt_2.50.3 deldir_1.0-6
## [47] sparseMatrixStats_1.6.0 vctrs_0.6.0
## [49] ensembldb_2.18.4 cachem_1.0.6
## [51] withr_2.5.0 Gviz_1.38.4
## [53] BSgenome_1.62.0 checkmate_2.1.0
## [55] GenomicAlignments_1.30.0 prettyunits_1.1.1
## [57] mclust_6.0.0 svglite_2.1.1
## [59] cluster_2.1.2 lazyeval_0.2.2
## [61] crayon_1.5.0 edgeR_3.36.0
## [63] pkgconfig_2.0.3 ProtGenerics_1.26.0
## [65] nnet_7.3-17 rlang_1.1.0
## [67] lifecycle_1.0.3 filelock_1.0.2
## [69] dichromat_2.0-0.1 rngtools_1.5.2
## [71] base64_2.0.1 Matrix_1.4-0
## [73] Rhdf5lib_1.16.0 base64enc_0.1-3
## [75] beeswarm_0.4.0 png_0.1-8
## [77] viridisLite_0.4.1 rjson_0.2.21
## [79] bitops_1.0-7 R.oo_1.25.0
## [81] KernSmooth_2.23-20 rhdf5filters_1.6.0
## [83] blob_1.2.4 DelayedMatrixStats_1.16.0
## [85] doRNG_1.8.6 stringr_1.5.0
## [87] nor1mix_1.3-0 readr_2.1.4
## [89] jpeg_0.1-10 scales_1.2.1
## [91] memoise_2.0.1 magrittr_2.0.2
## [93] plyr_1.8.8 zlibbioc_1.40.0
## [95] compiler_4.1.3 BiocIO_1.4.0
## [97] illuminaio_0.36.0 Rsamtools_2.10.0
## [99] cli_3.6.0 DSS_2.42.0
## [101] htmlTable_2.4.1 Formula_1.2-5
## [103] MASS_7.3-55 tidyselect_1.2.0
## [105] stringi_1.7.6 highr_0.9
## [107] yaml_2.3.5 askpass_1.1
## [109] latticeExtra_0.6-30 grid_4.1.3
## [111] sass_0.4.5 VariantAnnotation_1.40.0
## [113] tools_4.1.3 rstudioapi_0.13
## [115] foreign_0.8-82 bsseq_1.30.0
## [117] gridExtra_2.3 digest_0.6.29
## [119] BiocManager_1.30.16 shiny_1.7.4
## [121] Rcpp_1.0.10 siggenes_1.68.0
## [123] BiocVersion_3.14.0 later_1.3.0
## [125] org.Hs.eg.db_3.14.0 httr_1.4.2
## [127] AnnotationDbi_1.56.2 biovizBase_1.42.0
## [129] colorspace_2.1-0 rvest_1.0.3
## [131] XML_3.99-0.14 splines_4.1.3
## [133] statmod_1.5.0 multtest_2.50.0
## [135] systemfonts_1.0.4 xtable_1.8-4
## [137] jsonlite_1.8.0 R6_2.5.1
## [139] echarts4r_0.4.4 Hmisc_5.0-1
## [141] pillar_1.7.0 htmltools_0.5.4
## [143] mime_0.12 glue_1.6.2
## [145] fastmap_1.1.0 BiocParallel_1.28.3
## [147] interactiveDisplayBase_1.32.0 beanplot_1.3.1
## [149] codetools_0.2-18 utf8_1.2.2
## [151] lattice_0.20-45 bslib_0.4.2
## [153] tibble_3.1.6 curl_4.3.2
## [155] gtools_3.9.4 GO.db_3.14.0
## [157] openssl_2.0.0 interp_1.1-3
## [159] survival_3.3-1 rmarkdown_2.20
## [161] munsell_0.5.0 rhdf5_2.38.1
## [163] GenomeInfoDbData_1.2.7 impute_1.68.0
## [165] HDF5Array_1.22.1 gtable_0.3.3