readFrequencies {TarSeqQC} | R Documentation |
readFrequencies
builds a data frame containing the read frequencies
falling in targeted regions and out of those, separated by chromosome.
readFrequencies(object, BPPARAM = bpparam()) ## S4 method for signature 'TargetExperiment' readFrequencies(object, BPPARAM = bpparam())
object |
TargetExperiment class object. |
BPPARAM |
An optional BiocParallelParam instance defining the parallel back-end to be used during evaluation. |
data.frame 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) myReadPercentages<-readFrequencies(ampliPanel)