Plot read profiles for a particular feature.

Share:

Description

plotFeature plots the read profiles for a selected feature. 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

1
2
3
4
5
6
7
plotFeature(object, featureID, SNPs = TRUE, minAAF=0.05, minRD=10, xlab = "",
    title = "",  size = 0.5, BPPARAM = bpparam())

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

Arguments

object

TargetExperiment object.

featureID

Character indicating the ID of the feature.

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.

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

plotRegion

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
## 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)

# Exploring the read count profile for a particular amplicon
g<-plotFeature(ampliPanel, featureID="AMPL20")
if(interactive()){
g
}

Want to suggest features or report bugs for rdrr.io? Use the GitHub issue tracker.