Hi Mark and Hervé,
Thanks a lot. I will try that.
I was using strsplit(x,"|"), without the backslashes.

Thanks again.

Sincerely,
Hari


2009/6/16 Hervé Pagès <hpages@fhcrc.org>

> Hi Hari, Mark,
>
> Mark Robinson wrote:
>
>> Hi Hari.
>>
>> strsplit() will work, its just sensitive.  For starters, you might try:
>>
>>  > x <- c("ref|NM_004564|ref|PET112L:2131|mgc|BC130348:2158",
>> + "ref|NM_007266|ref|XAB1:2255|mgc|BC007451:2239","mgc|BC034752:79")
>>  >
>>  > strsplit(x,"\\|")
>> [[1]]
>> [1] "ref"           "NM_004564"     "ref"           "PET112L:2131"
>> [5] "mgc"           "BC130348:2158"
>>
>> [[2]]
>> [1] "ref"           "NM_007266"     "ref"           "XAB1:2255"
>> [5] "mgc"           "BC007451:2239"
>>
>> [[3]]
>> [1] "mgc"         "BC034752:79"
>>
>
> Note that it's better here to use strsplit() with fixed=TRUE. Then no
> need to escape the | and in addition strsplit() will be much faster...
>
> Cheers,
> H.
>
>
>
>>
>> And, for extracting the first 2 columns, maybe you'll want to migrate
>> towards something like:
>>
>>  > t(sapply(x, FUN=function(u) strsplit(u, "\\|")[[1]][1:2],
>> USE.NAMES=FALSE))
>>     [,1]  [,2]
>> [1,] "ref" "NM_004564"
>> [2,] "ref" "NM_007266"
>> [3,] "mgc" "BC034752:79"
>>
>> Hope that gets you started.
>>
>> Cheers,
>> Mark
>>
>>
>> On 17/06/2009, at 7:54 AM, Hari Easwaran wrote:
>>
>>  Hi all,
>>> I am working with Agilent microarray data and trying to extract only the
>>> accession numbers from the output probe annotation. Basically I have a
>>> column detailing the probe as follows:
>>>
>>> ref|NM_004564|ref|PET112L:2131|mgc|BC130348:2158
>>> ref|NM_007266|ref|XAB1:2255|mgc|BC007451:2239
>>> mgc|BC034752:79
>>> ref|NM_057094|ref|CRYBA2:-2513|ref|NM_005209:-2519|ref|NM_194302:45605|mirna|hsa-mir-375:5790
>>>
>>> ...
>>>
>>> I am trying to extract only the Refseq IDs (in this case NM_004564,
>>> NM_007266, NM_057094, NM_005209, NM_194302.....) and create a new column
>>> with the IDs. I am not able to figure out how to do this. I tried using
>>>  the
>>> function 'strsplit',  but it doesn't work.
>>> I am a newbie to R/Bioconductor and would appreciate if someone can help.
>>>
>>> Thanks.
>>> Hari
>>>
>>>    [[alternative HTML version deleted]]
>>>
>>> _______________________________________________
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>>>
>>
>> ------------------------------
>> Mark Robinson, PhD (Melb)
>> Epigenetics Laboratory, Garvan
>> Bioinformatics Division, WEHI
>> e: m.robinson@garvan.org.au
>> e: mrobinson@wehi.edu.au
>> p: +61 (0)3 9345 2628
>> f: +61 (0)3 9347 0852
>>
>> _______________________________________________
>> Bioconductor mailing list
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>>
>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M2-B876
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpages@fhcrc.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
>

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