working with .gmt files

Hi!

I have downloaded a pathway data set in .gmt format form the GSEA website.

I’m wondering how can I properly read this data set in R.

Could anyone help me?

Thank you!

You can read using read.gmt function from qusage package.

or by GSA.read.gmt function from GSA package.

you can try msigdbr package on cran.r-project.org/web/packages/msigdbr/vignettes/msigdbr-intro.html

it provides you with msigdb that compatable with fgsea and clusterProfiler. For example, I use it to do the fgea with human hallmark gene sets

library(msigdbr)
library(fgsea)

#Retrieve human H (hallmark gene sets) 
msigdbr_df <- msigdbr(species = "human", category = "H")


head(msigdbr_df)
# A tibble: 6 x 15
  gs_cat gs_subcat gs_name gene_symbol entrez_gene ensembl_gene human_gene_symb…
  <chr>  <chr>     <chr>   <chr>             <int> <chr>        <chr>           
1 H      ""        HALLMA… ABCA1                19 ENSG0000016… ABCA1           
2 H      ""        HALLMA… ABCB8             11194 ENSG0000019… ABCB8           
3 H      ""        HALLMA… ACAA2             10449 ENSG0000016… ACAA2           
4 H      ""        HALLMA… ACADL                33 ENSG0000011… ACADL           
5 H      ""        HALLMA… ACADM                34 ENSG0000011… ACADM           
6 H      ""        HALLMA… ACADS                35 ENSG0000012… ACADS      

# fixing format to work with fgsea
pathwaysH = split(x = msigdbr_df$entrez_gene, f = msigdbr_df$gs_name)

# run fgsea enrichment
fgseaRes <- fgsea(pathways=pathwaysH, ranks, ..)