R help - Jul 2013 - Subscript out of bound error

Hi All

I have a huge matrix m (10276 X 10276) dimension with same column name and
row names. (its a gene correlation matrix). I have another text file which
has 2700 names, basically locus ID of genes, which are also
rownames/colnames in m. Now I want to select all those columns from m whose
names match with the names in the text file and return ONLY those columns
and ALL the rows in a matrix format.
That is, the output should a matrix of dimension 10276 X 2700.

I have played around with subset and also tried all different methods like
reading the text file, converting to matrix and character and DF and tried
all possible ways I found on the web. The problem is that some of them work
on a smaller simulated dataset but says "Subscript out of bounds" 
when I
try on the bigger matrix(m).

Please help.. :(

Thanks!



-- 
*Chirag Gupta*
Department of Crop, Soil, and Environmental Sciences,
115 Plant Sciences Building, Fayetteville, Arkansas 72701

	[[alternative HTML version deleted]]

use 'match' to convert the names to column indices and then use that for
indexing

indx <- match(subCols, names(yourMatrix)
mySubset <- yourMatrix[, indx]

Sent from my iPad

On Jul 5, 2013, at 2:22, Chirag Gupta <cxg040 at email.uark.edu> wrote:
> Hi All
> 
> I have a huge matrix m (10276 X 10276) dimension with same column name and
> row names. (its a gene correlation matrix). I have another text file which
> has 2700 names, basically locus ID of genes, which are also
> rownames/colnames in m. Now I want to select all those columns from m whose
> names match with the names in the text file and return ONLY those columns
> and ALL the rows in a matrix format.
> That is, the output should a matrix of dimension 10276 X 2700.
> 
> I have played around with subset and also tried all different methods like
> reading the text file, converting to matrix and character and DF and tried
> all possible ways I found on the web. The problem is that some of them work
> on a smaller simulated dataset but says "Subscript out of bounds"
when I
> try on the bigger matrix(m).
> 
> Please help.. :(
> 
> Thanks!
> 
> 
> 
> -- 
> *Chirag Gupta*
> Department of Crop, Soil, and Environmental Sciences,
> 115 Plant Sciences Building, Fayetteville, Arkansas 72701
> 
>    [[alternative HTML version deleted]]
> 
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