plotRegion {TarSeqQC} | R Documentation

## Plot read profiles for a particular genomic region.

### Description

`plotRegion` plots the read profiles for a selected region. The minAAF parameter set the minimum proportion value to call an SNP and the minRD the minimum read depth. They are combined to obtain a minimum read count value at each position used to distinguish between possible SNPs and background noise. If SNPs is set as 'TRUE', colored bars will appear indicating the occurrence of possible SNPs surpassing the minAAF and minRD, at each genomic position.

### Usage

    plotRegion(object, region, seqname, SNPs = TRUE, minAAF=0.05, minRD=10,
        xlab = "", title = "", size = 0.5, BPPARAM = bpparam())

    ## S4 method for signature 'TargetExperiment'
    plotRegion(object, region, seqname, SNPs = TRUE,
        minAAF=0.05, minRD=10, xlab = "", title = "", size = 0.5,
        BPPARAM = bpparam())

### Arguments

`object` | TargetExperiment object.
`region` | Numeric of length two indicating the selected genomic region.
`seqname` | Character indicating the chromosome of the genomic region.
`SNPs` | Logical flag indicating if SNPs should be plotted.
`minAAF` | Numeric indicating the minimum alternative allele proportion necessary to call a SNP.
`minRD` | Numeric indicating the minimum read depth of alternative alleles necessary to call a SNP.
`xlab` | Character containing the axis x label.
`title` | Character containing the plot title.
`size` | Numeric indicating the size of line plots.
`BPPARAM` | An optional BiocParallelParam instance defining the parallel back-end to be used during evaluation.

### Value

ggplot2 graphics.

include TargetExperiment-FeatPerform.R

### 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

### See Also

`plotFeature`

### 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)

    # getting and exploring a sequenced region of a particular gene
    getRegion(ampliPanel, level="gene", ID="gene7", collapse=FALSE)
    # plot a particular genomic region
    g<-plotRegion(ampliPanel,region=c(4500,6800), seqname="chr10", SNPs=TRUE,
    xlab="", title="gene7 amplicons",size=0.5)
    # x11(type="cairo")
    if(interactive()){
    g
    }

[Package TarSeqQC version 1.14.0 Index]