R/ENCODE.R

In plbaldoni/mixNBHMM: Differential Peak Calling via Hidden Markov Model With Mixture of Negative Binomial Distributions

#' ChIP-seq read counts of H3K36me3 of GM12878, H1-hESC, and HepG2 cell lines (2 replicates each) from
#' chromosome 2.
#'
#' Data from the ENCODE Consortium of H3K36me3 ChIP-seq experiments (2 technical
#' replicates each) of GM12878, H1-hESC, and HepG2 cell lines from chromosome 2.
#' PCR duplicates were removed with 'samtools markdup'. Low quality reads were removed with
#' 'samtools view -q 10'. Read counts were tabulated using \code{mixNBHMMDataSetFromBam}.
#'
#' @docType data
#'
#' @usage data(ENCODE)
#'
#' @format RangedSummarizedExperiment
#'
#' @keywords datasets
#'
#' @references doi: 10.1093/nar/gkx1081
#'
#' @source
#' https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM733679
#' https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM733725
#' https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM733685
#'
#' @rawNamespace import(SummarizedExperiment, except = shift)
#'
#' @examples
#' data(ENCODE)
#' ENCODE
"ENCODE"