calculateDistance: Read BAM files and generate Euclidean distance data
In jonathonthill/MMAPPR2: Mutation Mapping Analysis Pipeline for Pooled RNA-Seq

Description Usage Arguments Value Examples

First step in the MMAPPR2 pipeline. Precedes the loessFit step.

1	calculateDistance(mmapprData)

mmapprData

The MmapprData object to be analyzed.

A MmapprData object with the distance slot filled.

if (requireNamespace('MMAPPR2data', quietly=TRUE)
        & all(Sys.which(c("samtools", "vep")) != "")) {
    mmappr_param <- MmapprParam(refFasta = MMAPPR2data::goldenFasta(),
                               wtFiles = MMAPPR2data::exampleWTbam(),
                               mutFiles = MMAPPR2data::exampleMutBam(),
                               species = "danio_rerio",
                               outputFolder = tempOutputFolder())

    md <- new('MmapprData', param = mmappr_param)
    postCalcDistMD <- calculateDistance(md)
}