calculateDistance: Read BAM files and generate Euclidean distance data

Description Usage Arguments Value Examples

View source: R/distance.R

Description

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

Usage

1
calculateDistance(mmapprData)

Arguments

mmapprData

The MmapprData object to be analyzed.

Value

A MmapprData object with the distance slot filled.

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
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)
}

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