Files: SaveResults

In Rolexa: Statistical analysis of Solexa sequencing data

Description

Read and write data in a convenient form for Rolexa base-calling

Usage

## S4 method for signature 'RolexaRun'
SaveResults(run=Rolexa.env,results,outpath,prefix="rs_")
SaveResults(run,...)
## S4 method for signature 'RolexaRun,SolexaPath'
CombineReads(run=Rolexa.env,path,pattern="s_[1-8]_0[01][0-9]*_seq*")
CombineReads(run,path,...)
## S4 method for signature 'RolexaRun,SolexaPath'
CombineFastQ(run=Rolexa.env,path,pattern="s_[1-8]_0[01][0-9]*",sext="_seq*",pext="_prb*")
CombineFastQ(run,path,...)

Arguments

run	a RolexaRun object defining the run parameters
results	a results list, as given by FilterResults or SeqScore
outpath	a directory name for the output files
path	a SolexaPath object
prefix	a prefix string for output file names
pattern	a pattern for selecting Solexa output files, see readXStringColumns
sext	file extension tag for sequence files readPrb
pext	file extension tag for prb files, see
...	additional arguments, ignored

Details

CombineReads reads "\_seq" files and splits the columns to create a ShortRead object, CombineFastQ reads "\_seq" and "\_prb" files and combines them into a ShortReadQ object, SaveResults creates a ShortReadQ objects from the output of FilterResults and writes it to a file using writeFastq.

Value

CombineReads returns a ShortRead object, CombineFastQ returns a ShortReadQ object,

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

readFastq to read fastq files, SeqScore and FilterResults to produce results for SaveResults

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