Turning GMT file into data frame so that third column is comma seperated

Question

Similar to: How to convert data in gmt format to dataframe?

I have downloaded a GMT file from the GSEA database (https://www.gsea-msigdb.org/gsea/msigdb/download_file.jsp?filePath=/msigdb/release/2022.1.Hs/c2.all.v2022.1.Hs.symbols.gmt)

I have imported this into R using the GSA.read.gmt tool from GSA as I want to do pathway analysis using GAUSS (https://github.com/diptavo/GAUSS/blob/master/example_gmt.txt).

GAUSS needs the table to have the genes in a comma separated manner as well as there being headers in the table.

I have tried using the gsub function on the third column but it doesn't work, I feel this is because a GMT file is not the same as a dataframe.

Would anyone be able to help me turn this column into a comma separated one please?

Many thanks

Answer 1

I used the unite function from tidyr but first I read the gmt file in as a data table using the read.delim function (with header set to False). Then I used unite:

library(tidyr)

gmt_file <- read.delim("~/path_to_file/file.gmt", header = F)
gmt_file <- gmt_file %>% unite(genes,3:ncol(gmt_file), sep=",")
colnames(gmt_file) <- c("pathway", "source", "genes")
write.table....