TarSeqQC (version 1.2.0)

setFeature<-: Setters for the TargetExperiment slots

Description

Set TargetExperiment slots, according to the given function call.

Usage

setFeature(object) <- value
"setFeature"(object) <- value
setAttribute(object) <- value
"setAttribute"(object) <- value
setScanBamP(object) <- value
"setScanBamP"(object) <- value
setPileupP(object) <- value
"setPileupP"(object) <- value
setFeaturePanel(object) <- value
"setFeaturePanel"(object) <- value
setGenePanel(object) <- value
"setGenePanel"(object) <- value
setBedFile(object) <- value
"setBedFile"(object) <- value
setBamFile(object) <- value
"setBamFile"(object) <- value
setFastaFile(object) <- value
"setFastaFile"(object) <- value

Arguments

object

TargetExperiment class object.

value

value to set the slot.

Value

a TargetExperiment object

Examples

## loading TargetExperiment object
if (interactive()){
    data(ampliPanel, package="TarSeqQC")
    ## Defining bam file, bed file and fasta file names and paths
    setBamFile(ampliPanel)<-system.file("extdata", "mybam.bam",
        package="TarSeqQC", mustWork=TRUE)
    setBedFile(ampliPanel)<-system.file("extdata", "mybed.bed",
        package="TarSeqQC", mustWork=TRUE)
    setFastaFile(ampliPanel)<-system.file("extdata", "myfasta.fa",
        package="TarSeqQC", mustWork=TRUE)
    ## Set feature slot value
    setFeature(ampliPanel)<-"amplicon"
    ## Set attribute slot value
    setAttribute(ampliPanel)<-"coverage"
    ## Set scanBamP slot value
    setScanBamP(ampliPanel)<-ScanBamParam()
    ## Set pileupP slot value
    setPileupP(ampliPanel)<-PileupParam()
    ## Set featurePanel slot value
    setFeaturePanel(ampliPanel)<-buildFeaturePanel(ampliPanel)
    ## Set genePanel slot value
    setGenePanel(ampliPanel)<-summarizePanel(ampliPanel)
    ## Set bedFile slot value
    setBedFile(ampliPanel)<-system.file("extdata", "mybed.bed",
        package="TarSeqQC", mustWork=TRUE)
    ## Set bamFile slot value
    setBamFile(ampliPanel)<-system.file("extdata", "mybam.bam",
        package="TarSeqQC", mustWork=TRUE)
    ## Set fastaFile slot value
    setFastaFile(ampliPanel)<-system.file("extdata", "myfasta.fa",
        package="TarSeqQC", mustWork=TRUE)
}