Question: (Closed) Extracting row and column names from matrix in R.
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kandoigaurav • 150 wrote:
I've two large matrices with p-values and correlation coefficients for lncRNA vs mRNA genes (both matrix have same structure, one has p-values while the other has corresponding correlation coefficients). I would like to extract all lncRNA-mRNA gene pairs for which the p-value is less than 0.05 and their corresponding correlation coefficients as well.
I'm using the following R script which gives me the row and column number, but I also want the names, i.e lncRNA and mRNA gene names:
Pmatrix = read.csv ("pmatrix.csv", header = FALSE) ##read the matrix with pvalues
sig_values <- which(Pmatrix<0.05, arr.in=TRUE) ##extract values less than 0.05
sig_values #list all (row,col) pairs with pvalues less than 0.05
Corr_Matrix = read.csv("corr_matrix.csv", header = FALSE) ##read the matrix with correlation values
Corr_Matrix[sig_values] ##list correlation values corresponding to pvalues less than 0.05.
This gives me a list of row and column numbers, but how can I get the names?
This is not really a bioinformatics question, it can be reduced to the generic R question: Extracting row and column names from matrix in R. (as you wrote yourself). Therefore it might be closed. Please read: ?rownames ?colnames. However you won't have any sensible col names, yours will be V1, V2, ... because of header=FALSE, and you won't have row.names either, because they were not defined during import, see ?read.csv and argument row.names.
In addition, the returned value of read.table is a data.frame not a matrix, as your variable names imply.
If you read https://cran.r-project.org/doc/manuals/r-release/R-data.html#Variations-on-read_002etable you should be prepared for these basic tasks.
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