[R] Printing row and column names of cells with specific value in a big matrix

[gaurav kandoi]

Thanks a lot Sarah. I think I've got what I wanted.

On Mon, Jul 20, 2015 at 2:55 PM, Sarah Goslee <sarah.goslee at gmail.com> wrote:
> Subsetting error. See below.
>
> On Mon, Jul 20, 2015 at 3:29 PM, gaurav kandoi <kandoigaurav at gmail.com> wrote:
>> Hi Sarah, sorry for posting in HTML.
>>
>> I've two big matrices (5k*4k) with the same structure, i.e. :
>>
>> ,mRNA1,mRNA2,mRNA3
>> lncRNA1,0.395646498,0.949950035,0.761770206
>> lncRNA2,0.037909944,0.661258022,0.558657799
>> lncRNA3,0.678459646,0.652364052,0.359053653
>>
>> Now, I would like to extract the names of the row,col pairs whose
>> value is less than 0.05. In this case, I should get the output as
>> (lncRNA2,mRNA1) and (lncRNA4,mRNA2) alongwith their values (0.03791
>> and 0.003). Since the structure of both the matrix is same, I would
>> also like to retrieve the corresponding values and row,col names from
>> the second matrix. (lncRNA2,mRNA1 and lncRNA4,mRNA2 alongwith their
>> values in the second matrix.)
>>
>> I'm using the following code:
>>
>>> Pmatrix = read.table("pmatrix.csv", header=T, sep="," , row.names=1)
>>> sig_values <- which(Pmatrix<0.05, arr.ind=TRUE)
>>> sig_values
>>> Corr_Matrix = read.csv("corr_matrix.csv", header = T, row.names=1)
>>> Corr_Matrix[sig_values]
>>
>> However, it only prints the row,col number (sig_values command) or
>> only the values (Corr_Matrix[sig_values]) command. How can I get the
>> row and column names alongwith their values?
>>
>> I've also tried printing using the following print command:
>>
>>>paste(rownames(Pmatrix)[sig_values[1]], colnames(Pmatrix)[sig_values[2]], sep=", ")
>
>> But it gives a output like this:
>>
>> [1] "lncRNA2, NA"
>
> Well, yes.
>
> sig_values[1]
>
>> sig_values[1]
> [1] 2
>> sig_values[2]
> [1] 8
>
> And there is no column 8, so no name.
>
> paste(rownames(Pmatrix)[sig_values[,1]],
> colnames(Pmatrix)[sig_values[,2]], sep=", ")
> [1] "lncRNA2, mRNA1" "lncRNA8, mRNA1" "lncRNA4, mRNA2" "lncRNA7,
> mRNA2" "lncRNA1, mRNA4"
> [6] "lncRNA3, mRNA4" "lncRNA5, mRNA5"
>
>> Sample input files available for download: https://goo.gl/xR6XDg
>
> dput() is preferred to expecting people to download things from unknown sources.
>
> Sarah
>
> --
> Sarah Goslee
> http://www.functionaldiversity.org



-- 
Gaurav Kandoi