I am interested in analyzing the enrichment of immune cell types in my RNA-seq data (human bulk biopsy samples) by using gene set variation analysis (GVSA). However, I am pretty lost with GSVA and GSEABase packages for R and do not know the structure of files that need to be prepared for GVSA (e.g. the gene set collection object).
I would like to use some pre-defined gene sets that identify immune cells which I retrieved from table S1A here: https://clincancerres.aacrjournals.org/content/suppl/2018/04/17/1078-0432.CCR-17-3509.DC1 to follow the GSVA molecular signature identification guide (4.1 in the GSVA guide here: https://www.bioconductor.org/packages/release/bioc/vignettes/GSVA/inst/doc/GSVA.pdf)
Could you give me a clue on how to prepare this gene set collection???
Thank you so much in advance!!!