buildFeaturePanel {TarSeqQC} | R Documentation

## 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())

    ## S4 method for signature 'TargetExperiment'
    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.

### Note

see full example in `TargetExperiment-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
    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)

[Package TarSeqQC version 1.10.0 Index]