generateCandidates: Generate potential causative mutations and consequences in...

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

Description

Follows the peakRefinement step and produces a MmapprData object ready for outputMmapprData.

Usage

generateCandidates(mmapprData)

Arguments

mmapprData

The MmapprData object to be analyzed.

Value

A MmapprData object with the candidates slot filled with a GRanges object for each peak chromosome containing variants and predicted consequences from Ensembl's Variant Effect Predictor.

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)

## End(Not run)

kjohnsen/MMAPPR2 documentation built on Oct. 1, 2019, 7:01 p.m.