[R] which question

[Richard Pearson]

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
>>
>> ______________________________________________
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>> 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
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