TargetExperiment-setters: Setters for the TargetExperiment slots

In gamerino/TarSeqQC: TARgeted SEQuencing Experiment Quality Control

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 [e-mail], Cristobal Fresno [e-mail], Yanina Murua [e-mail], Andrea S. Llera [e-mail] and Elmer A. Fernandez [e-mail]

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"

gamerino/TarSeqQC documentation built on Feb. 3, 2020, 9:19 p.m.