Retrieve gene sets from MSigDB

Usage

list_msigdb_versions()

list_msigdb_collections(version = NULL)

choose_msigdb_collection(version)

get_msigdb(
  version = choose_msigdb_version(),
  collection = choose_msigdb_collection(version),
  gene_id_type = c("entrez", "symbols"),
  as_table = FALSE
)

Arguments

version: The MSigDB version. The value can be obtained by list_msigdb_versions(). If this argument is not specified, a menu will be printed to let users to select.
collection: The gene set collection. The values can be obtained by list_msigdb_collections().
gene_id_type: One of "entrez" and "symbols".
as_table: Whether to return a list or a table.

Examples

list_msigdb_versions()
#>  [1] "6.0"       "6.1"       "6.2"       "7.0"       "7.1"       "7.2"      
#>  [7] "7.3"       "7.4"       "7.5.1"     "7.5"       "2022.1.Hs" "2022.1.Mm"
#> [13] "2023.1.Hs" "2023.1.Mm" "2023.2.Hs" "2023.2.Mm" "2024.1.Hs" "2024.1.Mm"
list_msigdb_collections("2024.1.Hs")
#>  [1] "c1.all"             "c2.all"             "c2.cgp"            
#>  [4] "c2.cp.biocarta"     "c2.cp.kegg_legacy"  "c2.cp.kegg_medicus"
#>  [7] "c2.cp.pid"          "c2.cp.reactome"     "c2.cp"             
#> [10] "c2.cp.wikipathways" "c3.all"             "c3.mir.mir_legacy" 
#> [13] "c3.mir.mirdb"       "c3.mir"             "c3.tft.gtrd"       
#> [16] "c3.tft.tft_legacy"  "c3.tft"             "c4.3ca"            
#> [19] "c4.all"             "c4.cgn"             "c4.cm"             
#> [22] "c5.all"             "c5.go.bp"           "c5.go.cc"          
#> [25] "c5.go.mf"           "c5.go"              "c5.hpo"            
#> [28] "c6.all"             "c7.all"             "c7.immunesigdb"    
#> [31] "c7.vax"             "c8.all"             "h.all"