outputMmapprData: Generate plots and tables from MMAPPR2 data

In jonathonthill/MMAPPR2: Mutation Mapping Analysis Pipeline for Pooled RNA-Seq

Description

Generate plots and tables from MMAPPR2 data

Usage

outputMmapprData(mmapprData)

Arguments

mmapprData

The MmapprData object to be output

Value

A MmapprData object after writing output files to the folder specified in the outputFolder slot of the link{MmapprParam} used.

Examples

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())
}
## Not run: 
md <- new('MmapprData', param = mmappr_param)
postCalcDistMD <- calculateDistance(md)
postLoessMD <- loessFit(postCalcDistMD)
postPrePeakMD <- prePeak(postLoessMD)
postPeakRefMD <- peakRefinement(postPrePeakMD)
postCandidatesMD <- generateCandidates(postPeakRefMD)

outputMmapprData(postCandidatesMD)

## End(Not run)

jonathonthill/MMAPPR2 documentation built on Oct. 2, 2019, 8:16 a.m.