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Last data update: 2014.03.03

R: Diagnostic plots

CombinedPlot

R Documentation

Diagnostic plots

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)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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> library(Rolexa)
Error in library(Rolexa) : there is no package called 'Rolexa'
Execution halted