Retrieve the gene sets data frame

Retrieve a data frame of gene sets and their member genes. The available species and collections can be checked with msigdbr_species() and msigdbr_collections().

Usage

msigdbr(species = "Homo sapiens", category = NULL, subcategory = NULL)

Arguments

species

Species name, such as Homo sapiens or Mus musculus.

category

MSigDB collection abbreviation, such as H or C1.

subcategory

MSigDB sub-collection abbreviation, such as CGP or BP.

Value

A data frame of gene sets with one gene per row.

References

https://www.gsea-msigdb.org/gsea/msigdb/collections.jsp

Examples

# get all human gene sets
# \donttest{
msigdbr(species = "Homo sapiens")
#> # A tibble: 4,029,754 × 15
#>    gs_cat gs_subcat      gs_name        gene_symbol entrez_gene ensembl_gene   
#>    <chr>  <chr>          <chr>          <chr>             <int> <chr>          
#>  1 C3     MIR:MIR_LEGACY AAACCAC_MIR140 ABCC4             10257 ENSG00000125257
#>  2 C3     MIR:MIR_LEGACY AAACCAC_MIR140 ABRAXAS2          23172 ENSG00000165660
#>  3 C3     MIR:MIR_LEGACY AAACCAC_MIR140 ACTN4                81 ENSG00000130402
#>  4 C3     MIR:MIR_LEGACY AAACCAC_MIR140 ACVR1                90 ENSG00000115170
#>  5 C3     MIR:MIR_LEGACY AAACCAC_MIR140 ADAM9              8754 ENSG00000168615
#>  6 C3     MIR:MIR_LEGACY AAACCAC_MIR140 ADAMTS5           11096 ENSG00000154736
#>  7 C3     MIR:MIR_LEGACY AAACCAC_MIR140 AMER2            219287 ENSG00000165566
#>  8 C3     MIR:MIR_LEGACY AAACCAC_MIR140 ANK2                287 ENSG00000145362
#>  9 C3     MIR:MIR_LEGACY AAACCAC_MIR140 API5               8539 ENSG00000166181
#> 10 C3     MIR:MIR_LEGACY AAACCAC_MIR140 ATOSA             56204 ENSG00000047346
#> # ℹ 4,029,744 more rows
#> # ℹ 9 more variables: human_gene_symbol <chr>, human_entrez_gene <int>,
#> #   human_ensembl_gene <chr>, gs_id <chr>, gs_pmid <chr>, gs_geoid <chr>,
#> #   gs_exact_source <chr>, gs_url <chr>, gs_description <chr>
# }

# get mouse C2 (curated) CGP (chemical and genetic perturbations) gene sets
# \donttest{
msigdbr(species = "Mus musculus", category = "C2", subcategory = "CGP")
#> # A tibble: 378,935 × 18
#>    gs_cat gs_subcat gs_name                 gene_symbol entrez_gene ensembl_gene
#>    <chr>  <chr>     <chr>                   <chr>             <int> <chr>       
#>  1 C2     CGP       ABBUD_LIF_SIGNALING_1_… Ahnak             66395 ENSMUSG0000…
#>  2 C2     CGP       ABBUD_LIF_SIGNALING_1_… Alcam             11658 ENSMUSG0000…
#>  3 C2     CGP       ABBUD_LIF_SIGNALING_1_… Ankrd40           71452 ENSMUSG0000…
#>  4 C2     CGP       ABBUD_LIF_SIGNALING_1_… Arid1a            93760 ENSMUSG0000…
#>  5 C2     CGP       ABBUD_LIF_SIGNALING_1_… Bckdhb            12040 ENSMUSG0000…
#>  6 C2     CGP       ABBUD_LIF_SIGNALING_1_… AU021092         239691 ENSMUSG0000…
#>  7 C2     CGP       ABBUD_LIF_SIGNALING_1_… Capn9             73647 ENSMUSG0000…
#>  8 C2     CGP       ABBUD_LIF_SIGNALING_1_… Cd24a             12484 ENSMUSG0000…
#>  9 C2     CGP       ABBUD_LIF_SIGNALING_1_… Cyfip1            20430 ENSMUSG0000…
#> 10 C2     CGP       ABBUD_LIF_SIGNALING_1_… Dcaf11            28199 ENSMUSG0000…
#> # ℹ 378,925 more rows
#> # ℹ 12 more variables: human_gene_symbol <chr>, human_entrez_gene <int>,
#> #   human_ensembl_gene <chr>, gs_id <chr>, gs_pmid <chr>, gs_geoid <chr>,
#> #   gs_exact_source <chr>, gs_url <chr>, gs_description <chr>, taxon_id <int>,
#> #   ortholog_sources <chr>, num_ortholog_sources <dbl>
# }