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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