Retrieve Organism-specific MSigDB Gene Sets
get_mgsigdb_gsets(
species = "Homo sapiens",
db_species = "HS",
collection = NULL,
subcollection = NULL
)Retrieves the MSigDB gene sets and returns a list containing 2 elements:
gene_sets - A list containing the genes involved in each of the selected MSigDB gene sets
descriptions - A named vector containing the descriptions for each selected MSigDB gene set
species name for output genes, such as Homo sapiens, Mus musculus, etc.
See msigdbr_species for all the species available in
the msigdbr package.
Species abbreviation for the human or mouse databases ("HS" or "MM").
collection. e.g., H, C1. (default = NULL,
i.e. list all gene sets in collection).
See msigdbr_collections for all available options
the msigdbr package.
sub-collection, such as CGP, BP, etc. (default = NULL,
i.e. list all gene sets in collection).
See msigdbr_collections for all available options
the msigdbr package.
this function utilizes the function msigdbr
from the msigdbr package to retrieve the 'Molecular Signatures Database'
(MSigDB) gene sets (Subramanian et al. 2005 <doi:10.1073/pnas.0506580102>,
Liberzon et al. 2015 <doi:10.1016/j.cels.2015.12.004>).
Available collections are: H: hallmark gene sets, C1: positional gene sets,
C2: curated gene sets, C3: motif gene sets, C4: computational gene sets,
C5: GO gene sets, C6: oncogenic signatures and C7: immunologic signatures