TarSeqQC (version 1.2.0)

plotInOutFeatures: Function to explore read percentages in targeted regions and out targeted regions.

Description

plotInOutFeatures allows the graphical exploration of the data frame obtained using readPercentages. This data frame contains information about amount of reads mapped into the targeted regions and out of them. This information is presented in rows, one for each chromosome and in absolute and relative amounts. After it invokation, a bar plot built as a ggplot object is returned

Usage

plotInOutFeatures(object, ...)
"plotInOutFeatures"(object, absolute = FALSE)
"plotInOutFeatures"(object, absolute = FALSE, BPPARAM = bpparam())

Arguments

object

a data frame or a TargetExperiment.

...

additional parameters according to the function call

absolute

logical indicating if absoulte frequency should be used.

BPPARAM

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

Value

ggplot object.

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)

g<-plotInOutFeatures(ampliPanel)