MU101188 MU101310 MU101326 MU10251
MU101188 1 0 0 0
MU101310 0 1 0 1
MU101326 0 1 1 0
MU10251 1 0 0 1
I need to extract all pairs of MU ids for which the value is equal to 1. I m using the following R script which gives me the row and column number, but I also want the names
Pmatrix = read.csv ("file.csv", header = TRUE, row.names = 1)
sig_values <- which(Pmatrix==1, arr.in= TRUE)
Using your approach, subset colnames and rownames by index:
cbind.data.frame(
colIDs = colnames(Pmatrix)[ sig_values[, 1] ],
rowIDs = rownames(Pmatrix)[ sig_values[, 2] ])
# colIDs rowIDs
# 1 MU101188 MU101188
# 2 MU101310 MU101310
# 3 MU101326 MU101326
# 4 MU10251 MU10251
Or using tidyverse, reshape from wide-to-long then filter:
library(tidyverse)
Pmatrix %>%
rownames_to_column("id") %>%
gather(key = "key", value = "value", -id) %>%
filter(value == 1)
# id key value
# 1 MU101188 MU101188 1
# 2 MU101310 MU101310 1
# 3 MU101326 MU101326 1
# 4 MU10251 MU10251 1
Error in read.table(file = file, header = header, sep = sep, quote = quote, : duplicate 'row.names' are not allowed
Error says you have duplicated rownames, see related SO post:
Log in to answer this question.
Hello xxxxxxxx!
It appears that your post has been cross-posted to another site: https://stackoverflow.com/q/55702350/680068
This is typically not recommended as it runs the risk of annoying people in both communities.