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

In TarSeqQC: TARgeted SEQuencing Experiment Quality Control

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 [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
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)

TarSeqQC documentation built on Nov. 8, 2020, 6:03 p.m.