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

Description Usage Arguments Value Note Author(s) Examples

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

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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

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## 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)

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