MMD {MMDiff2} | R Documentation

## DBAmmd Object for Cfp1 example

### Description

DBAmmd Object for Cfp1 example

### Usage

    data('MMD')

### Examples

    # 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)

[Package MMDiff2 version 1.16.0 Index]