Description Usage Arguments Details Author(s) References See Also Examples
Generate summary plots of the results of a base calling batch
1 2 3 4 5 6 7 8 | ## 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))
|
run |
a |
int |
a |
seq |
a |
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 |
Four types of diagnostic plots can be selected with the what
argument of BatchAnalysis
:
length
shows the
histogram of tag lengths,
information
the distribution of information content per
sequenced base, namely ((2*length(tag)-total_entropy(tag))/nb_cycles)
,
base
the base composition of the sequences,
ratio
the ratio of
complementary bases,
iupac
the 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
.
Jacques Rougemont, Arnaud Amzallag, Christian Iseli, Laurent Farinelli, Ioannis Xenarios, Felix Naef
Probabilistic base calling of Solexa sequencing data, BMC Bioinformatics 2008, 9:431
SaveResults
to save the results produced by
SeqScore
or FilterResults
.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 | 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)
|
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