helas3: ENCODE ChIP-seq broad data from Helas3 cell line

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

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

plbaldoni/epigrahmm documentation built on Oct. 14, 2023, 5:13 a.m.