[R] Problem with Grep Under Loop

[Gundala Viswanath]

Dear all,

This is the sample of the source data (tab delimited)

http://dpaste.com/82660/plain/

- Gundala Viswanath
Jakarta - Indonesia



On Mon, Oct 6, 2008 at 9:05 PM, Gustaf Rydevik <gustaf.rydevik at gmail.com> wrote:
> On Mon, Oct 6, 2008 at 1:37 PM, Gundala Viswanath <gundalav at gmail.com> wrote:
>> Dear all,
>>
>> I have no problem with this individual grep command:
>>
>>> datk <- grep("XM_528056", source$V1)
>>> dat2 <- source[datk,]
>>> print(dat2)
>>             V1      V2   V3 V4      V5      V6         V7
>> 35995 XM_528056 panTro2 chr8  + 1775569 1896107 Chimpanzee
>>
>>
>> BUT, when I run them under the loop it gives this error:
>>
>>
>>> hm_acc <- c("XM_528056","AB002296")
>>> for (i in 1:length(hm_acc)){
>> +
>> +    hm_acc_id <- as.character(hm_acc[i])
>> +    print(hm_acc_id)
>> +
>> +    hm_allk <- grep(hm_acc_id,source$V1)
>> +    hm_all <- source[hm_allk,]
>> +
>> +    print(hm_all)
>> + }
>>
>> [1] "XM_528056"
>> [1] V1 V2 V3 V4 V5 V6 V7
>> <0 rows> (or 0-length row.names)
>> [1] "AB002296"
>> [1] V1 V2 V3 V4 V5 V6 V7
>> <0 rows> (or 0-length row.names)
>> .....
>>
>> What's wrong with my way of using grep?
>> Please advice.
>>
>>
>> - Gundala Viswanath
>> Jakarta - Indonesia
>>
>
>
> Hi,
>
> Could you give us a small sample of the "source" data, so that your
> example is reproducible?
> From looking at your code, it seems as if you copied something wrong.
> First you write:
>  grep("XM_528056", source$V1)
>
> ,but when you print dat2 it seems as if your ID-code ("XM_528056") is
> in V2, not V1.
>
>
> regards,
>
> Gustaf
>
>
> --
> Gustaf Rydevik, M.Sci.
> tel: +46(0)703 051 451
> address:Essingetorget 40,112 66 Stockholm, SE
> skype:gustaf_rydevik
>