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

[Martin Morgan]

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,

Martin

> David
>
> 	[[alternative HTML version deleted]]
>
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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