library(methylKit) library(data.table) library(GenomicRanges) file.list <- list('/Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methylKit/M1.txt','/Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methylKit/M3.txt', '/Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methylKit/T1D3.txt', '/Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methylKit/T1D5.txt', '/Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methylKit/T3D3.txt', '/Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methylKit/T3D5.txt') myobj=read(file.list,sample.id=list("1_sperm","2_sperm","1_72hpf","1_120hpf","2_72hpf","2_120hpf"),assembly="v9",treatment=c(1,0,1,1,0,0)) meth<-unite(myobj) head(meth) nrow(meth) getCorrelation(meth,plot=T) hc<- clusterSamples(meth, dist="correlation", method="ward", plot=T) PCA<-PCASamples(meth)