prePeak: Identify chromosomes containing peaks

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

Description

Follows the loessFit step and precedes peakRefinement.

Usage

prePeak(mmapprData)

Arguments

mmapprData

The MmapprData object to be analyzed.

Value

A MmapprData object with the peaks slot initalized.

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)

## End(Not run)

MMAPPR2 documentation built on Nov. 8, 2020, 6:53 p.m.