Plots1: Batch Analysis

In Rolexa: Statistical analysis of Solexa sequencing data

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

See Also

SaveResults to save the results produced by SeqScore or FilterResults.

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)

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