mmappr: Mutation Mapping Analysis Pipeline for Pooled RNA-Seq

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

Description

MMAPPR2 is designed to map the causative mutation in a forward genetics screen. It analyzes aligned sequence files, calculates the per-base Euclidean distance between the mutant and wild-type pools, performs a Loess regression on that distance, and generates candidate variants in regions of peak distance.

Usage

mmappr(mmapprParam)

Arguments

mmapprParam

A MmapprParam object containing desired parameters.

Value

A MmapprData object containing results and/or intermediate data.

See Also

calculateDistance, loessFit, prePeak, peakRefinement, generateCandidates, outputMmapprData

Examples

if (requireNamespace('MMAPPR2data', quietly = TRUE)
        & all(Sys.which(c('vep', 'samtools')) != '')) {

    # Specify parameters:
    mmappr_param <- MmapprParam(refFasta = MMAPPR2data::goldenFasta(),
                               wtFiles = MMAPPR2data::exampleWTbam(),
                               mutFiles = MMAPPR2data::exampleMutBam(),
                               species = "danio_rerio",
                               outputFolder = tempOutputFolder())

    # Run pipeline:
    mmapprData <- mmappr(mmappr_param)

}
## Not run: 
### Alternately, you can navigate the pipeline step by step.
### This may be helpful for debugging.
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)

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