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

[Sarah Goslee]

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