TarSeqQC (version 1.2.0)

buildFeaturePanel: Function to build a feature panel based on specific genomic regions.

Description

buildFeaturePanel builds panel slots of a TargetExperiment object. Input can be a bam file or a pileup matrix. If the bed file contains a high number of amplicons, the bam file as input is recommended in order to diminish memory requirements. The resulting object is a GRanges instance having panel and counts/coverage information.

Usage

buildFeaturePanel(object, BPPARAM = bpparam())
"buildFeaturePanel"(object, BPPARAM = bpparam())

Arguments

object

TargetExperiment class object.

BPPARAM

An optional BiocParallelParam instance defining the parallel back-end to be used during evaluation.

Value

GRanges object.

Examples

if (interactive()) {
    ## loading TargetExperiment object
    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)
    setFastaFile(ampliPanel)<-system.file("extdata", "myfasta.fa",
        package="TarSeqQC", mustWork=TRUE)
    myFeaturePanel<-buildFeaturePanel(ampliPanel)
}