Script to translate mouse or human gene id gmt files to the opposite organism.
The first time you run the script, it will try to automatically check and/or install the required packages.
To run the script:
./translatorGMT.R -i input.gmt -d mouse2hum_biomart_ens87.txt -t HS/MS -o output.gmt -c TRUE/FALSE
Option -t: HS to translate gmt to from mouse to human. MS to translate gmt from human to mouse
Option -c: when translating to mouse, 0 keeps genes as normal, 1 capitalizes the gene name (i.e. FALSE:Kras, TRUE:KRAS)
Whenever one gene from one organism matches multiple genes id from the other, all genes from the last will be added to the new gmt file.
E.g. input Mouse gmt contains (Dcaf4), the output Human gmt will contain (DCAF4, DCAF4L2, DCAF4L1)
The mouse2hum_biomart_ens87.txt file was obtained from: http://genomespot.blogspot.com.es/2016/12/msigdb-gene-sets-for-mouse.html The file mouse2hum_biomart_ens87_reduced.txt contains the same information (gene ids) without taking into account the name of transcripts (as this is a shorter table it will let the script to perform faster).