helas3 {epigraHMM} | R Documentation |
Data from EZH2, H3K27me3, and H3K36me3 ChIP-seq data from Helas3 cell line. For illustrative purposes, the data has been subset to chromosome 19. The dataset contains two replicates from each mark.
data(helas3)
An object of class "epigraHMMDataSet"
.
Davis et al. (2018) NAR 46(D1):D794-D801. (PubMed)
# # # The data 'helas3' was created as follows. # options(timeout=9999999) # # url <- 'http://hgdownload.soe.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/' # samples <- c('wgEncodeBroadHistoneHelas3H3k36me3StdAlnRep1.bam', # 'wgEncodeBroadHistoneHelas3H3k36me3StdAlnRep2.bam', # 'wgEncodeBroadHistoneHelas3H3k27me3StdAlnRep1.bam', # 'wgEncodeBroadHistoneHelas3H3k27me3StdAlnRep2.bam', # 'wgEncodeBroadHistoneHelas3Ezh239875AlnRep1.bam', # 'wgEncodeBroadHistoneHelas3Ezh239875AlnRep2.bam') # # input <- paste0(url,samples) # output <- paste0(tempdir(),samples) # # for(idx in seq_len(length(input))){ # download.file(url = input[idx],destfile = output[idx]) # download.file(url = paste0(input[idx],'.bai'), # destfile = paste0(output[idx],'.bai')) # } # # gr <- segmentGenome(genome = 'hg19', # window = 1000,rm.gap = TRUE,rm.blacklist = TRUE) # # cData <- data.frame(condition = rep(c('H3K36me3','H3K27me3','EZH2'),each = 2), # replicate = rep(c(1,2),times = 3)) # # subGr <- gr[seqnames(gr) == 'chr19' & start(gr) >= 40e6 & end(gr) <= 50e6] # # helas3 <- # epigraHMMDataSetFromBam(bamFiles = output,colData = cData, # genome = subGr,windowSize = 1000) data(helas3) helas3