Thanks this worked well! Ingunn >-----Original Message----- >From: Martin Morgan [mailto:[email protected]] >Sent: Tuesday, August 04, 2009 5:45 PM >To: Ingunn Berget >Cc: bioC >Subject: Re: [Bioc-sig-seq] readAligned in ShortRead package > >Martin Morgan wrote: >> 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]] > >oops! quotes in quality strings will mess up parsing, and we're after >column 12. So this should be > >what[[12]] <- character() >contig <- scan(path_to_file, what=what, sep="\t", > fill=TRUE, quote="")[[12]] > >> ## 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 > > >-- >Martin Morgan >Computational Biology / Fred Hutchinson Cancer Research Center >1100 Fairview Ave. N. >PO Box 19024 Seattle, WA 98109 > >Location: Arnold Building M1 B861 >Phone: (206) 667-2793
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