Thanks a lot Sarah. I think I've got what I wanted. On Mon, Jul 20, 2015 at 2:55 PM, Sarah Goslee <sarah.gos...@gmail.com> wrote: > Subsetting error. See below. > > On Mon, Jul 20, 2015 at 3:29 PM, gaurav kandoi <kandoigau...@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 ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.