TargetExperiment-readFrequencies: Function to explore read frequencies in targeted regions and...

In TarSeqQC: TARgeted SEQuencing Experiment Quality Control

Description

readFrequencies builds a data frame containing the read frequencies falling in targeted regions and out of those, separated by chromosome.

Usage

readFrequencies(object, BPPARAM = bpparam())

## S4 method for signature 'TargetExperiment'
readFrequencies(object, BPPARAM = bpparam())

Arguments

object	TargetExperiment class object.
BPPARAM	An optional BiocParallelParam instance defining the parallel back-end to be used during evaluation.

Value

data.frame 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)

myReadPercentages<-readFrequencies(ampliPanel)

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