BatchAnalysis {Rolexa}R Documentation

Batch Analysis

Description

Generate summary plots of the results of a base calling batch

Usage

BatchAnalysis(results, what=c("length","information","base","ratio","iupac"),main='')
QualityBoxPlots(results, cycles = 1:Rolexa.env$nSequencingLength, par = list(las=2))

Arguments

results for BatchAnalysis: a 6*n matrix with cluster coordinates (four columns), sequences (fifth column) and entropy scores (sixth column). For QualityBoxPlots: columns 5+cycles contain per-base quality scores.
what select one the plot types
main a title for the plot
cycles the list of cycles to plot
par parameters for the plotting function

Details

Four types of diagnostic plots can be selected with the what argument of BatchAnalysis:

QualityBoxPlots makes boxplots of quality scores along the sequences

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

See Also

LoadResults to read results files, SaveResults to save the results produced by SeqFitScore or SeqEvalScore.

Examples

library(Rolexa.demo)
data(one_tile)
seqscore = SeqFitScore(int=int,colonies=1:50)
par(ask=TRUE)
BatchAnalysis(results=seqscore,what="iupac")
BatchAnalysis(results=seqscore,what="information")
results = FilterResults(seqscore)
BatchAnalysis(results=results,what="length")
QualityBoxPlots(results=cbind(seq,fastq), cycles = 1:35)
[Package Rolexa version 1.1.7 Index]