Re: [R] which question

From: Richard Pearson <richard.pearson_at_postgrad.manchester.ac.uk>
Date: Fri, 06 Jun 2008 15:41:49 +0100

I didn't get any attached data, but my suspicion here is that you have somehow got RefSeq IDs in column 8 of human, as well as the gene symbols. Did you read this data in from a text file?

Eleni Christodoulou wrote:
> An example is:
>
> symbol=human[which(human[,3] %in% genes.sam.names),8]
>
> The data* human* and *genes.sam.names* are attached. The result of the above
> command is:

>> symbol

> [1] CCL18 MARCO SYT13
> [4] FOXC1 CDH3
> [7] CA12 CELSR1 NM_018440
> [10] MICROTUBULE-ASSOCIATED NM_015529 ESR1
> [13] PHGDH GABRP LGMN
> [16] MMP9 BMP7 KLF5
> [19] RIPK2 GATA3 NM_032023
> [22] TRIM2 CCND1 MMP12
> [25] LDHB AF493978 SOD2
> [28] SOD2 SOD2 NME5
> [31] STC2 RBP1 ROPN1
> [34] RDH10 KRTHB1 SLPI
> [37] BBOX1 FOXA1 NM_005669
> [40] MCCC2 CHI3L1 GSTM3
> [43] LPIN1 DSC2 FADS2
> [46] ELF5 CYP1B1 LMO4
> [49] AL035297 NM_152398 AB018342
> [52] PIK3R1 NFKBIE MLZE
> [55] NFIB NM_052997 NM_006023
> [58] CPB1 CXCL13 CBR3
> [61] NM_017527 FABP7 DACH
> [64] IFI27 ACOX2 CXCL11
> [67] UGP2 CLDN4 M12740
> [70] IGKC IGKC CLECSF12
> [73] AY069977 HOXB2 SOX11
> [76] NM_017422 TLR2
> [79] CKS1B BC017946 APOBEC3B
> [82] HLA-DRB1 HLA-DQB1
> [85] CCL13 C4orf7
> [88] NM_173552
> 21345 Levels: (2 (32 (55.11 (AIB-1) (ALU (CAK1) (CAP4) (CASPASE ... ZYX
>
> As you can see, apart from gene symbols, which is the required thing, RefSeq
> ID sare also retrieved...
>
> Thanks a lot,
> Eleni
>
>
>
>
>
>
> On Fri, Jun 6, 2008 at 1:23 PM, Dieter Menne <dieter.menne_at_menne-biomed.de>
> wrote:
>
>> Eleni Christodoulou <elenichri <at> gmail.com> writes:
>>
>>> I was trying to select a column of a data frame using the *which*
>> command. I
>>> was actually selecting the rows of the data frame using *which, *and then
>>> displayed a certain column of it. The command that I was using is:
>>> sequence=*mydata*[*which*(human[,3] %in% genes.sam.names),*9*]
>> ....
>> Please provide a running example. The *mydata* are difficult to read.
>>
>>
>> Dieter
>>
>> ______________________________________________
>> R-help_at_r-project.org mailing list
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>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>

>
> [[alternative HTML version deleted]]
>
> ______________________________________________
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> and provide commented, minimal, self-contained, reproducible code.
>
-- 
Richard D. Pearson             richard.pearson_at_postgrad.manchester.ac.uk
School of Computer Science,    http://www.cs.man.ac.uk/~pearsonr
University of Manchester,      Tel: +44 161 275 6178
Oxford Road,                   Mob: +44 7971 221181
Manchester M13 9PL, UK.        Fax: +44 161 275 6204

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Received on Fri 06 Jun 2008 - 17:12:54 GMT

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