[R] subsetting data file by intoducing a second file

[Eik Vettorazzi]

Hi Ozgul,
the interesting part is the "select" parameter in subset:

subset(bg,select=c_bg[,1])


cheers

Am 12.02.2013 15:29, schrieb Ozgul Inceoglu:
> Hello,
> 
> I have a very data matrix and I have a file which has the names that I need to subset. However I cannot manage to subset the main file. ANy idea?
> 
> bg <- read.table (file.choose(), header=T, row.names)
> bg
>           Otu00022 Otu00029 Otu00039 Otu00042 Otu00101 Otu00105 Otu00125 Otu00131 Otu00137 Otu00155 Otu00158 Otu00172 Otu00181 Otu00185 Otu00190 Otu00209 Otu00218
> Gi20Jun11  0.001217        0 0.001217        0 0.000000        0        0        0 0.001217        0        0        0        0        0 0.001217        0 0.001217
> Gi40Jun11  0.000000        0 0.000000        0 0.000000        0        0        0 0.000000        0        0        0        0        0 0.000000        0 0.000000
> Gi425Jun11 0.000000        0 0.000000        0 0.000000        0        0        0 0.000000        0        0        0        0        0 0.000000        0 0.000000
> Gi45Jun11  0.000000        0 0.000000        0 0.001513        0        0        0 0.000000        0        0        0        0        0 0.000000        0 0.000000
> Gi475Jun11 0.000000        0 0.000000        0 0.000000        0        0        0 0.000000        0        0        0        0        0 0.000000        0 0.000000
> Gi50Jun11  0.000000        0 0.000000        0 0.000000        0        0        0 0.000000        0        0        0        0        0 0.000000        0 0.000000
> ...
> #second file which has the names that I want to subset
> c_bg
>       [,1]     
>   [1,] "Otu0128"
>   [2,] "Otu0218"
>   [3,] "Otu0034"
>   [4,] "Otu0257"
>   [5,] "Otu0212"
>   [6,] "Otu0279"
>   [7,] "Otu0318"
>   [8,] "Otu0266"
>   [9,] "Otu0056"
> ...
> #by using the c_bg name file, I would like to subset bg file
> 
> g1<-subset(bg,colnames(bg) %in% (c_bg))
> 
> # this returns me the all the column names in bg file.
> 
> Thank you,
> Ö
> 
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Eik Vettorazzi
Institut für Medizinische Biometrie und Epidemiologie
Universitätsklinikum Hamburg-Eppendorf

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