source("https://bioconductor.org/biocLite.R")
biocLite("MMDiff2")
library('MMDiff2')
library('MMDiffBamSubset')
ExperimentData <- list(genome='BSgenome.Mmusculus.UCSC.mm9',
dataDir=system.file("extdata", package="MMDiffBamSubset"),
sampleSheet="Cfp1.csv")
MetaData <- list('ExpData' = ExperimentData)
MMD <- DBAmmd(MetaData)
data("Cfp1-Peaks")
MMD <- setRegions(MMD,Peaks)
MMD <- getPeakReads(MMD)
MMD <- estimateFragmentCenters(MMD)
MMD <- compHists(MMD)
MMD <- compDists(MMD)
MMD <- setContrast(MMD,contrast='byCondition')
MMD <- compPvals(MMD)
res <- reportResults(MMD)
