Cfp1-Peaks {MMDiff2} | R Documentation |
Subset of MACS called Peaks for Cfp-1 data set. Consensus Peaks were created using diffBind (see below).
data('Cfp1-Peaks')
contains Peaks, a GRanges object with 500 ranges and 3 metadata columns
data taken from Clouaire et al., Genes and Development, 2012.
# data was created as follows: ## Not run: library('MMDiffBamSubset') dataDir <- system.file("extdata", package="MMDiffBamSubset") library('DiffBind') olddir <- setwd(dataDir) DBA <- dba(sampleSheet="Cfp1.csv", minOverlap=3) Peaks <- dba.peakset(DBA, bRetrieve = TRUE) DBA <- dba.count(DBA, minOverlap=3) setwd(olddir) peaks <- dba.peakset(DBA, bRetrieve=TRUE) C <- Counts(MMD) idx <- which(C[,1]>150 & C[,3]>150&width(Peaks)>1000&width(Peaks)<5000) Peaks <- Peaks[idx[1:500]] ## End(Not run)