Rolexa (version 1.28.0)

CombinedPlot: Diagnostic plots

Description

Generate plots to visualy assess the quality of select colonies or sequencing cycles

Usage

"CombinedPlot"(run=Rolexa.env, int, seq, scores, colonies = 1:4, par = list())
CombinedPlot(run,...)
"ChannelHistogram"(int, cycles = c(1,18,36),
threemodes = FALSE, par = list())
ChannelHistogram(int,...)

Arguments

run

a RolexaRun object defining the run parameters

int

a SolexaIntensity object

seq

a ShortRead object

scores

a matrix of base quality scores (one column per base, one row per sequence)

cycles

the list of cycles to plot

colonies

the list of rows to select for plotting

threemodes

fit and plot a mixture of 3 gaussians (2 by default)

par

parameters for the plotting function

...

additional arguments, ignored

Details

CombinedPlot creates one plot for each selected colony with the sequence along the x axis, the four intensities plotted as barplots above each base and the quality scores as a line plot below the sequence.

ChannelHistogram plots histograms and signal-noise thresholds for each of the four intensity channels on selected cycles. Fits to 2 or 3 gaussians are overlaid on the histograms.

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 = CombineFastQ(run=rolenv,path=path)
CombinedPlot(run=rolenv,int=int,seq=seq,scores=as(quality(seq),"matrix"),colonies=1)