[R] Filtering a dataset's columns by another dataset's column names

[David Winsemius]

So you want the data that is in Dataset 1 but only the column names  
that are also in Dataset 2:

How about:

  subset(DS1, select = names(DS1) %in% names(DS2) )

 > DS1 <-read.table(textConnection("Individual    SNP1    SNP2     
SNP3    SNP4    SNP5
+ 1    A    G    T    C    A
+ 2    T    C    A    G    T
+ 3    A    C    T    C    A"),header=TRUE)
 > DS2 <-read.table(textConnection("Individual    SNP1    SNP3     
SNP5    SNP6    SNP7
+ 4    A    T    T    G    C
+ 5    T    A    A    G    G
+ 6    A    A    T    C    G"),header=TRUE)

 > subset(DS1, select= names(DS1) %in% names(DS2) )
   Individual SNP1 SNP3 SNP5
1          1    A    T    A
2          2    T    A    T
3          3    A    T    A

Tested!
-- 
David Winsemius
Heritage Labs

On Feb 27, 2009, at 12:27 PM, Josh B wrote:

> Hello all,
>
> I hope some of you can come to my rescue, yet again.
>
> I have two genetic datasets, and I want one of the datasets to have  
> only the columns that are in common with the other dataset.
> Here is a toy example (my real datasets have hundreds of columns):
>
> Dataset 1:
>
> Individual    SNP1    SNP2    SNP3    SNP4    SNP5
> 1    A    G    T    C    A
> 2    T    C    A    G    T
> 3    A    C    T    C    A
>
> Dataset 2:
>
> Individual    SNP1    SNP3    SNP5    SNP6    SNP7
> 4    A    T    T    G    C
> 5    T    A    A    G    G
> 6    A    A    T    C    G
>
> I want Dataset1 to have only columns that are also represented in  
> Dataset 2, i.e., I want to generate a new Dataset 3 that looks like  
> this:
>
> Individual    SNP1    SNP3    SNP5
> 1    A    T    A
> 2    T    A    T
> 3    A    T    A
>
> Does anyone know how I could do this? Keep in mind that this is not  
> a simple merge, as in the "merge" function.
>
> Thanks very much for your help everyone.
> Josh B.
>
>
>
>
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>
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