MMD {MMDiff2} | R Documentation |
DBAmmd Object for Cfp1 example
data('MMD')
# data was created as follows: ## Not run: library('MMDiff2') library('MMDiffBamSubset') # create metaData: 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,pairedEnd=FALSE, run.parallel=FALSE) MMD <- DBAmmd(MetaData) MMD <- setRegions(MMD,Peaks) MMD <- getPeakReads(MMD,pairedEnd=FALSE, run.parallel=FALSE) MMD <- estimateFragmentCenters(MMD, shift=NULL, draw.on=FALSE) MMD <- compHists(MMD, bin.length=20) MMD <- compDists(MMD, dist.method = "MMD", run.parallel = FALSE) group1 <- Samples(MMD)$Condition==1 names(group1) <- Samples(MMD)$SampleID group2 <- Samples(MMD)$Condition==2 names(group2) <- Samples(MMD)$SampleID con <- list(group1=group1, group2=group2, name1='WT-Resc', name2='KO') MMD <- compPvals(MMD, contrasts=list(con)) ## End(Not run)