Last data update: 2014.03.03

R: Plot nucleotide read percentages for a particular feature.
plotNtdPercentageR Documentation

Plot nucleotide read percentages for a particular feature.

Description

plotNtdPercentage plots the percentages of the ocurrence of each nucleotide in each position for a selected feature.

Usage

plotNtdPercentage(object, featureID, BPPARAM = bpparam())

## S4 method for signature 'TargetExperiment'
plotNtdPercentage(object, featureID,
    BPPARAM = bpparam())

Arguments

object

a TargetExperiment object.

featureID

a character indicating the feature ID.

BPPARAM

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

returned by the function.

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 and Elmer A. Fernandez efernandez@bdmg.com.ar

See Also

plotFeature

Examples

if(interactive()){
## 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 nucleotide percentages compositions of the read counts for a
# particular amplicon
g<-plotNtdPercentage(ampliPanel,featureID="AMPL20")
g
}

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(TarSeqQC)
Loading required package: GenomicRanges
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector
Loading required package: ggplot2
Loading required package: plyr

Attaching package: 'plyr'

The following object is masked from 'package:XVector':

    compact

The following object is masked from 'package:IRanges':

    desc

The following object is masked from 'package:S4Vectors':

    rename

Loading required package: openxlsx
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/TarSeqQC/TargetExperiment-plotNtdPercentage.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotNtdPercentage
> ### Title: Plot nucleotide read percentages for a particular feature.
> ### Aliases: plotNtdPercentage plotNtdPercentage,TargetExperiment-method
> ###   plotNtdPercentage-methods
> 
> ### ** Examples
> 
> #if(interactive()){
> ## 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 nucleotide percentages compositions of the read counts for a
> # particular amplicon
> g<-plotNtdPercentage(ampliPanel,featureID="AMPL20")
   |                                                                               |                                                                      |   0%   |                                                                               |===================================                                   |  50%   |                                                                               |======================================================================| 100%

   |                                                                               |                                                                      |   0%   |                                                                               |===================================                                   |  50%   |                                                                               |======================================================================| 100%

> g
> #}
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>