Hi, Laura,

In the meantime perhaps you could give this a try:

https://stat.ethz.ch/pipermail/r-help/2006-September/112953.html

Just us setwd("/this/is/my/folder") to move to the folder holing your 
files. I guess "c:/your/folder/here" must work on a Windows box.

This doesn't solve the "extra four heading lines issue" though. But I am 
pretty sure if want be hard to cut they out prior to concatenate the files.

Please, Laurent, have you this function reading files as byte streams 
already implemented in R? Thanks!

Cheers,

Ricardo


Laura Rodriguez Murillo wrote:
> Hi,
>
> Thank you for your email. As soon as I get some free time I'll try to
> learn some perl. See what I can do with these files.
>
> Laura
>
> 2008/11/7 laurent <lgautier@gmail.com>:
>   
>> Such files do exceed the capabilities of most machines.
>>
>> One way I helped someone with a similar problem was to hack a script
>> (Python or Perl come to my mind for such jobs, but it is possible to
>> implement it in R if you like) that read the files as byte streams
>> rather than line per line.
>>
>> This way it run with a minimal memory footprint (and will on Microsoft
>> Windows... if the resulting file size does not exceed the capabilities
>> of the OS).
>>
>>
>> L.
>>
>> On Fri, 2008-11-07 at 13:38 -0500, Laura Rodriguez Murillo wrote:
>>     
>>> 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@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@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
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Bioconductor mailing list
>>>>>>> Bioconductor@stat.math.ethz.ch
>>>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>>>>> Search the archives:
>>>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>>>>>
>>>>>>>
>>>>>>>               
>>>>>> --
>>>>>> 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@robarts.ca
>>>>>> http://www.lrgc.ca
>>>>>>
>>>>>>
>>>>>>
>>>>>>             
>>>>> _______________________________________________
>>>>> Bioconductor mailing list
>>>>> Bioconductor@stat.math.ethz.ch
>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>>> Search the archives:
>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>>>           
>>>>         
>>> _______________________________________________
>>> Bioconductor mailing list
>>> Bioconductor@stat.math.ethz.ch
>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>       
>>     
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>
>
>   

-- 
Ricardo Rodríguez
Your EPEC Network ICT Team


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