Rolexa (version 1.28.0)

BatchAnalysis: Batch Analysis

Description

Generate summary plots of the results of a base calling batch

Usage

"PlotCycles"(run=Rolexa.env, int, seq,
cycles=c(1,11,21,31), par=list())
PlotCycles(run,...)
"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.

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)