plotInOutFeatures {TarSeqQC} | R Documentation

## Function to explore read percentages in targeted regions and out targeted regions.

### 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 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

### 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)

[Package TarSeqQC version 1.14.0 Index]