helas3 {epigraHMM} | R Documentation

## ENCODE ChIP-seq broad data from Helas3 cell line

### Description

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.

### Usage

    data(helas3)

### Format

An object of class `"epigraHMMDataSet"`.

### Source

ENCODE Broad Histone

### References

Davis et al. (2018) NAR 46(D1):D794-D801. (PubMed)

### 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

[Package epigraHMM version 1.0.8 Index]