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