MmapprParam-functions: MmapprParam Getters and Setters

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

Description

Access and assign slots of MmapprParam object.

Usage

## S4 method for signature 'MmapprParam'
refFasta(obj)

## S4 method for signature 'MmapprParam'
wtFiles(obj)

## S4 method for signature 'MmapprParam'
mutFiles(obj)

## S4 method for signature 'MmapprParam'
species(obj)

## S4 method for signature 'MmapprParam'
vepFlags(obj)

## S4 method for signature 'MmapprParam'
refGenome(obj)

## S4 method for signature 'MmapprParam'
homozygoteCutoff(obj)

## S4 method for signature 'MmapprParam'
distancePower(obj)

## S4 method for signature 'MmapprParam'
peakIntervalWidth(obj)

## S4 method for signature 'MmapprParam'
minDepth(obj)

## S4 method for signature 'MmapprParam'
minBaseQuality(obj)

## S4 method for signature 'MmapprParam'
minMapQuality(obj)

## S4 method for signature 'MmapprParam'
loessOptResolution(obj)

## S4 method for signature 'MmapprParam'
loessOptCutFactor(obj)

## S4 method for signature 'MmapprParam'
naCutoff(obj)

## S4 method for signature 'MmapprParam'
outputFolder(obj)

## S4 method for signature 'MmapprParam'
fileAggregation(obj)

## S4 replacement method for signature 'MmapprParam'
refFasta(obj) <- value

## S4 replacement method for signature 'MmapprParam'
wtFiles(obj) <- value

## S4 replacement method for signature 'MmapprParam'
mutFiles(obj) <- value

## S4 replacement method for signature 'MmapprParam'
vepFlags(obj) <- value

## S4 replacement method for signature 'MmapprParam'
refGenome(obj) <- value

## S4 replacement method for signature 'MmapprParam'
species(obj) <- value

## S4 replacement method for signature 'MmapprParam'
homozygoteCutoff(obj) <- value

## S4 replacement method for signature 'MmapprParam'
distancePower(obj) <- value

## S4 replacement method for signature 'MmapprParam'
peakIntervalWidth(obj) <- value

## S4 replacement method for signature 'MmapprParam'
minDepth(obj) <- value

## S4 replacement method for signature 'MmapprParam'
minBaseQuality(obj) <- value

## S4 replacement method for signature 'MmapprParam'
loessOptResolution(obj) <- value

## S4 replacement method for signature 'MmapprParam'
loessOptCutFactor(obj) <- value

## S4 replacement method for signature 'MmapprParam'
naCutoff(obj) <- value

## S4 replacement method for signature 'MmapprParam'
outputFolder(obj) <- value

## S4 replacement method for signature 'MmapprParam'
minMapQuality(obj) <- value

## S4 replacement method for signature 'MmapprParam'
fileAggregation(obj) <- value

Arguments

obj	Desired MmapprParam object.
value	Value to replace desired attribute.

Value

The desired MmapprParam attribute.

See Also

MmapprParam

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(mmappr_param) <- 'mmappr2_test_1'
    minBaseQuality(mmappr_param) <- 25
    vepFlags(mmappr_param)
}

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