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Last data update: 2014.03.03

R: Batch Analysis

BatchAnalysis

R Documentation

Batch Analysis

Description

Generate summary plots of the results of a base calling batch

Usage

## S4 method for signature 'RolexaRun'
PlotCycles(run=Rolexa.env, int, seq,
cycles=c(1,11,21,31), par=list())
PlotCycles(run,...)
## S4 method for signature 'RolexaRun'
BatchAnalysis(run=Rolexa.env, seq, scores, what=c("length","information","base","ratio","iupac"), main='')
BatchAnalysis(run,...)
QualityBoxPlots(run=Rolexa.env, seq, cycles, par=list(las=2))

Arguments

`run`	a `RolexaRun` object defining the run parameters
`int`	a `SolexaIntensity` object
`seq`	a `DNAStringSet` object
`scores`	a matrix of base quality scores (one column per base, one row per sequence)
`what`	select one the plot types
`main`	a title for the plot
`cycles`	the cycles to plot
`par`	parameters for the plotting functions
`...`	additional arguments, ignored

Details

Four types of diagnostic plots can be selected with the what argument of BatchAnalysis:

lengthshows the histogram of tag lengths,
informationthe distribution of information content per sequenced base, namely ((2*length(tag)-total_entropy(tag))/nb_cycles),
basethe base composition of the sequences,
ratiothe ratio of complementary bases,
iupacthe proportion of the different classes of ambiguous bases along the sequences.

QualityBoxPlots makes boxplots of quality scores along the sequences. PlotCycles will execute SeqScore with plot=TRUE.

Author(s)

Jacques Rougemont, Arnaud Amzallag, Christian Iseli, Laurent Farinelli, Ioannis Xenarios, Felix Naef

References

Probabilistic base calling of Solexa sequencing data, BMC Bioinformatics 2008, 9:431

Examples

path = SolexaPath(system.file("extdata", package="ShortRead"))
rolenv = SetModel(idsep="_")
int = readIntensities(path,pattern="s_1_0001",withVariability=FALSE)
seq = CombineReads(run=rolenv,path=path,pattern="s_1_0001_seq*")
results = SeqScore(run=rolenv,int=int,seqInit=seq,cycles=1:36)
PlotCycles(run=rolenv,int=int,seq=seq,cycles=1:4)
par(ask=TRUE)
BatchAnalysis(rolenv,sread(seq),matrix(),what="iupac")
BatchAnalysis(rolenv,sread(seq),results$entropy,what="information")
results = FilterResults(run=rolenv,results=results)
BatchAnalysis(rolenv,sread(seq),results,what="length")
seq = readFastq(path)
par(mar=c(4,4,1,1),cex=1.5,lwd=2)
QualityBoxPlots(rolenv,seq,cycles=10:36)

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)

R is free software and comes with ABSOLUTELY NO WARRANTY.
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Type 'license()' or 'licence()' for distribution details.

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Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(Rolexa)
Error in library(Rolexa) : there is no package called 'Rolexa'
Execution halted