Get gene sets — get_gene_sets • aquarius

This function is used to get gene sets of interest from MSigDB

Usage

get_gene_sets(
  species = "Mus musculus",
  gs_cat = c("H", "C2", "C5"),
  gs_subcat = c("", "GO:BP", "GO:MF", "GO:CC", "CP:KEGG", "CP:WIKIPATHWAYS",
    "CP:REACTOME", "CP:PID"),
  gs_subcat_short = c("HALLMARK", "BP", "MF", "CC", "KEGG", "WP", "REACTOME", "PID"),
  gs_subcat_long = c("Hallmark", "GO : Biological Processes", "GO : Molecular Functions",
    "GO : Cellular Components", "KEGG Pathways", "Wiki Pathways", "Reactome",
    "Pathways Interaction")
)

Arguments

species: CHARACTER : a species, for species parameter in msigdbr::sigdbr function (default to "Mus musculus")
gs_cat: CHARACTER VECTOR : gene sets category to keep (default to c("H", "C2", "C5"))
gs_subcat: CHARACTER VECTOR : gene sets subcategory to keep. It must be NULL to keep everything, or a subset of possible category in gs_cat (default to c("", "GO:BP", "GO:MF", "GO:CC", "CP:KEGG", "CP:WIKIPATHWAYS", "CP:REACTOME", "CP:PID"))
gs_subcat_short: CHARACTER VECTOR : New names for each value in gs_subcat, so should be the same length as gs_subcat. It adds a new column category in the output. It must be NULL to be skipped.
gs_subcat_long: CHARACTER VECTOR : New names for each value in gs_subcat, so should be the same length as gs_subcat. It must be NULL to be skipped.

Value

A list with three elements :

gene_sets_full is the full database associated with species
gene_sets is the subset of the full database containing gene sets of interest
long_names is a list made with gs_subcat_short and gs_subcat_long