Subsetting error. See below. On Mon, Jul 20, 2015 at 3:29 PM, gaurav kandoi <[email protected]> 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 ______________________________________________ [email protected] 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.
