[BioC] Problems reading multiple MAQ map files with ShortRead ReadAligned

Martin Morgan mtmorgan at fhcrc.org
Fri Mar 20 12:59:42 CET 2009

David Rossell <david.rossell at irbbarcelona.org> writes:

> Hi, I'm using ShortRead package version 1.0.7 on R 2.8.0.
> I have three binary map files produced by MAQ that I want to read into
> Bioconductor. I can read one file at a time with the function ReadAligned,
> by typing
> aln <- readAligned(dir,"S1.map",type="MAQMap")
> This works like a charm. However, I cannot read all files in the directory
>> aln <- readAligned(dirPath=dir,type="MAQMap")
> Error: UserArgumentMismatch
>   'dirPath', 'pattern' must be 'character(1)'
> I tried specifying the pattern argument but the function still doesn't work.
>> aln <- readAligned(dirPath=dir,pattern="S.*",type="MAQMap")
> Error: UserArgumentMismatch
>   'dirPath', 'pattern' must be 'character(1)'
> Is this a bug or am I doing something wrong? Any ideas/help are most
> welcome.

neither, it's a design inconsistency that should be smoothed out --
the MAQ binary files are read in one at a time; you can use 'append'
on the results to combine them.

aln <- append(readAligned(dirPath, "s_1.map", type="MAQMap"),
              readAligned(dirPath, "s_2.map", type="MAQMap"))

For these whole-lane files a more typical work flow is to process one
lane (e.g., filter + coverage) into a much smaller data structure, and
then perhaps collate the results. Along the lines of

doALane <- function(dirPath, fileName)
    # read and process a lane
dataDir <- "/some/path"
runs <- lapply(list.files(dataDir), doALane, dirPath=dataPath)
# combine elements of run as necessary

Hope that helps,


> David
> 	[[alternative HTML version deleted]]
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M2 B169
Phone: (206) 667-2793

More information about the Bioconductor mailing list