gaurav kandoi
2015-Jul-20 17:44 UTC
[R] Printing row and column names of cells with specific value in a big matrix
Hi All
I've two big matrices (5k*4k) with the same structure, i.e. :
mRNA1 mRNA2 mRNA3 lncRNA1 0.395646 0.94995 0.76177 lncRNA2 0.03791
0.661258 0.558658 lncRNA3 0.67846 0.652364 0.359054 lncRNA4 0.57769 0.003
0.459127
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?
Regards
--
*Gaurav Kandoi*
[[alternative HTML version deleted]]
Sarah Goslee
2015-Jul-20 19:11 UTC
[R] Printing row and column names of cells with specific value in a big matrix
Without a reproducible example, or at least a non-mangled one (please don't post in HTML), I'm not inclined to try it, but why not use sig_values to index row.names() and col.names() if you're after the names? Sarah On Mon, Jul 20, 2015 at 1:44 PM, gaurav kandoi <kandoigaurav at gmail.com> wrote:> Hi All > > I've two big matrices (5k*4k) with the same structure, i.e. : > > mRNA1 mRNA2 mRNA3 lncRNA1 0.395646 0.94995 0.76177 lncRNA2 0.03791 > 0.661258 0.558658 lncRNA3 0.67846 0.652364 0.359054 lncRNA4 0.57769 0.003 > 0.459127 > 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? > > Regards > > -- > *Gaurav Kandoi* > > [[alternative HTML version deleted]]-- Sarah Goslee http://www.functionaldiversity.org
gaurav kandoi
2015-Jul-20 19:29 UTC
[R] Printing row and column names of cells with specific value in a big matrix
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" Sample input files available for download: https://goo.gl/xR6XDg Regards On Mon, Jul 20, 2015 at 2:11 PM, Sarah Goslee <sarah.goslee at gmail.com> wrote:> Without a reproducible example, or at least a non-mangled one (please > don't post in HTML), I'm not inclined to try it, but why not use > sig_values to index row.names() and col.names() if you're after the > names? > > Sarah > > On Mon, Jul 20, 2015 at 1:44 PM, gaurav kandoi <kandoigaurav at gmail.com> wrote: >> Hi All >> >> I've two big matrices (5k*4k) with the same structure, i.e. : >> >> mRNA1 mRNA2 mRNA3 lncRNA1 0.395646 0.94995 0.76177 lncRNA2 0.03791 >> 0.661258 0.558658 lncRNA3 0.67846 0.652364 0.359054 lncRNA4 0.57769 0.003 >> 0.459127 >> 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? >> >> Regards >> >> -- >> *Gaurav Kandoi* >> >> [[alternative HTML version deleted]] > > -- > Sarah Goslee > http://www.functionaldiversity.org-- Gaurav Kandoi