buildFeaturePanel {TarSeqQC} | R Documentation |
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.
buildFeaturePanel(object, BPPARAM = bpparam()) ## S4 method for signature 'TargetExperiment' buildFeaturePanel(object, BPPARAM = bpparam())
object |
TargetExperiment class object. |
BPPARAM |
An optional BiocParallelParam instance defining the parallel back-end to be used during evaluation. |
GRanges object.
see full example in TargetExperiment-class
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
## 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)