setFeature<- {TarSeqQC} | R Documentation

## Setters for the TargetExperiment slots

### Description

Set TargetExperiment slots, according to the given function call.

Set TargetExperimentList slots, according to the given function call.

### Usage

    setFeature(object) <- value

    ## S4 replacement method for signature 'TargetExperiment,character'
    setFeature(object) <- value

    setAttribute(object) <- value

    ## S4 replacement method for signature 'TargetExperiment,character'
    setAttribute(object) <- value

    setScanBamP(object) <- value

    ## S4 replacement method for signature 'TargetExperiment,ScanBamParam'
    setScanBamP(object) <- value

    setPileupP(object) <- value

    ## S4 replacement method for signature 'TargetExperiment,PileupParam'
    setPileupP(object) <- value

    setFeaturePanel(object) <- value

    ## S4 replacement method for signature 'TargetExperiment,GRanges'
    setFeaturePanel(object) <- value

    setGenePanel(object) <- value

    ## S4 replacement method for signature 'TargetExperiment,GRanges'
    setGenePanel(object) <- value

    setBedFile(object) <- value

    ## S4 replacement method for signature 'TargetExperiment,character'
    setBedFile(object) <- value

    setBamFile(object) <- value

    ## S4 replacement method for signature 'TargetExperiment,character'
    setBamFile(object) <- value

    setFastaFile(object) <- value

    ## S4 replacement method for signature 'TargetExperiment,character'
    setFastaFile(object) <- value

    ## S4 replacement method for signature 'TargetExperimentList,character'
    setFeature(object) <- value

### Arguments

`object` | TargetExperiment class object.
`value` | value to set the slot.

### Value

a TargetExperiment object

### Note

see full example in `TargetExperiment-class`

see full example in `TargetExperimentList-class`

### Author(s)

Gabriela A. Merino gmerino@bdmg.com.ar, Cristobal Fresno cfresno@bdmg.com.ar, Yanina Murua ymurua@leloir.org.ar, Andrea S. Llera allera@leloir.org.ar and Elmer A. Fernandez efernandez@bdmg.com.ar

### 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()
    }
    ## loading TargetExperimentList object
    data(TEList, package="TarSeqQC")
    ## Set feature slot value
    setFeature(TEList)<-"amplicon"

[Package TarSeqQC version 1.16.0 Index]