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

In gamerino/TarSeqQC: TARgeted SEQuencing Experiment Quality Control

Description

plotInOutFeatures allows the graphical exploration of the data frame obtained using readFrequencies. This data frame contains information about the amount of reads mapped to 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 invocation, a bar plot built as a ggplot object is returned

Usage

plotInOutFeatures(object, ...)

## S4 method for signature 'data.frame'
plotInOutFeatures(object, absolute = FALSE)

## S4 method for signature 'TargetExperiment'
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 absolute frequency should be used.
BPPARAM	An optional BiocParallelParam instance defining the parallel back-end to be used during evaluation.

Value

ggplot 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)

g<-plotInOutFeatures(ampliPanel)

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