Plots1: Batch Analysis

Description Usage Arguments Details Author(s) References See Also Examples

Description

Generate summary plots of the results of a base calling batch

Usage

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## 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:

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

See Also

SaveResults to save the results produced by SeqScore or FilterResults.

Examples

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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)

Rolexa documentation built on Oct. 5, 2016, 4:38 a.m.