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
>
> _______________________________________________
> Bioc-sig-sequencing mailing list
> [email protected]
> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
_______________________________________________
Bioc-sig-sequencing mailing list
[email protected]
https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
