[BioC] how to put together 600 files from the 5.0 Affy SNPchip

Laura Rodriguez Murillo laura.lmurillo at gmail.com
Fri Nov 7 19:38:47 CET 2008


Benilton,
Thank you. Unfortunately, the paste command doesn't work with these
big files. Does this only work with R under unix or is it possible in
windows?. Otherwise, I'll try with R when I get back to the unix
machine.

Laura

2008/11/7 Benilton Carvalho <bcarvalh at jhsph.edu>:
> Laura,
>
> if you're running *NIX, can't you just use the bash command "paste"?
>
> if you really want to use R, assume you have names of your files in the
> variable "files", then something like:
>
> ## This goes in R and assumes you're running *NIX
> cmd <- paste("paste", paste(files, collapse=" "), "> output.txt")
> system(cmd)
>
> later, you can just get rid of the first 4 lines of output.txt.
>
> b
>
> On Nov 7, 2008, at 3:04 PM, Laura Rodriguez Murillo wrote:
>
>> David,
>>
>> Thank you for your reply. I had tried with this software but it
>> doesn't recognize my files, it looks as it doesn't like .txt files.
>> Any idea?
>>
>> Laura
>>
>> 2008/11/6 David Carter <dcarter at robarts.ca>:
>>>
>>> Hi Laura,
>>> Affymetrix has a free tool (free and easy to download) called Genotyping
>>> Console that will export 1 file for all your samples with SNPs on rows
>>> and
>>> samples on columns.  I haven't tried it with 622 samples though...
>>> Sincerely,
>>> David Carter
>>>
>>>
>>> Laura Rodriguez Murillo wrote:
>>>>
>>>> Hi,
>>>> I'm new in this mailing list and  also using bioconductor. I'd
>>>> appreciate your feedback on this: I have 622 files that correspond to
>>>> 622 samples genotyped for the SNPs in the 5.0 SNPChip from Affymetrix.
>>>> Each file consists of two columns of almost 500 K rows (plus 4 lines
>>>> at the begining that I won't need). The number of rows are the same in
>>>> every file. I would need to put all these files together, where the
>>>> first column is common to all of them (SNP names) (so I just need it
>>>> once in the big file). Once I have all the columns one after the other
>>>> I would also need to paste a column with the chromosome number for
>>>> each SNP (which is in another file, just this info alone). Do you know
>>>> if there's any way to do this with Bioconductor?.
>>>>
>>>> Thank you!
>>>>
>>>> Laura
>>>>
>>>> _______________________________________________
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>>>>
>>>>
>>>
>>> --
>>> David Carter
>>> Facility Manager
>>> London Regional Genomics Centre
>>> Robarts Research Institute, Room 4.01
>>> PO Box 5015, 100 Perth Drive
>>> London, Ontario, Canada, N6A 5K8
>>>
>>> phone:  519-663-3253
>>> fax:    519-663-3037
>>>
>>> dcarter at robarts.ca
>>> http://www.lrgc.ca
>>>
>>>
>>>
>>
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>



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