[Bioc-sig-seq] readAligned in ShortRead package

[Martin Morgan]

Ingunn Berget wrote:
> Dear All
> 
> According to the documentation for "readAligned" in package "ShortRead" (version 1.2.1) the match contig column is ignored, is there any easy way of getting this information into R?

as a work-around, these are text files and you might try

## read
aln <- readAligned(path_to_file, type="SolexaExport")
what <- rep(list(NULL), 22)
what[[8]] <- "character"
contig <- scan(path_to_file, what=what, sep="\t", fill=TRUE)[[8]]
## check contig for correct values

## add to alignData
adata <- alignData(aln)
adata[["contig", labelDescription="Solexa export 'contig' data"]] <-
  contig

## update AlignedRead
aln <- initialize(aln, alignData=adata)

If the files are gz-compressed, then I think you'll want to

contig <- scan(gzfile(path_to_file), what=what, sep="\t",
               fill=TRUE)[[8]]

I will update ShortRead to parse this data into alignData.

Martin

> 
> 
> Best regards 
> Ingunn
> 
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