R/data-helas3.R

In plbaldoni/epigrahmm: Epigenomic R-based analysis with hidden Markov models

#' ENCODE ChIP-seq broad data from Helas3 cell line
#'
#' 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.
#'
#' @docType data
#'
#' @usage data(helas3)
#'
#' @format An object of class \code{"epigraHMMDataSet"}.
#'
#' @keywords datasets
#'
#' @references Davis et al. (2018) NAR 46(D1):D794-D801.
#' (\href{https://pubmed.ncbi.nlm.nih.gov/29126249/}{PubMed})
#'
#' @source \href{http://hgdownload.soe.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHistone/}{ENCODE Broad Histone}
#'
#' @examples
#' # # # 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
"helas3"