Plots2: Diagnostic plots

In Rolexa: Statistical analysis of Solexa sequencing data

Description

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

Usage

## S4 method for signature 'RolexaRun'
CombinedPlot(run=Rolexa.env, int, seq, scores, colonies = 1:4, par = list())
CombinedPlot(run,...)
## S4 method for signature 'SolexaIntensity'
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.

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

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)

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