Retrieve a data frame of gene sets and their member genes. The original human genes can be converted into their corresponding counterparts in various model organisms, including mouse, rat, pig, zebrafish, fly, and yeast. The output includes gene symbols along with NCBI and Ensembl IDs.
Usage
msigdbr(
db_species = "HS",
species = "human",
collection = NULL,
subcollection = NULL,
category = deprecated(),
subcategory = deprecated()
)
Arguments
- db_species
Species abbreviation for the human or mouse databases (
"HS"
or"MM"
).- species
Species name for output genes, such as
"Homo sapiens"
or"Mus musculus"
. Both scientific and common names are acceptable. Usemsigdbr_species()
for the available options.- collection
Collection abbreviation, such as
"H"
or"C1"
. Usemsigdbr_collections()
for the available options.- subcollection
Sub-collection abbreviation, such as
"CGP"
or"BP"
. Usemsigdbr_collections()
for the available options.- category
- subcategory
Value
A tibble (a data frame with class tibble::tbl_df
) of gene sets with one gene per row.
Details
Historically, the MSigDB resource has been tailored to the analysis of human-specific datasets, with gene sets exclusively aligned to the human genome. Starting with release 2022.1, MSigDB incorporated a database of mouse-native gene sets and was split into human and mouse divisions ("Hs" and "Mm"). Each one is provided in the approved gene symbols of its respective species.
Mouse MSigDB includes gene sets curated from mouse-centric datasets and specified in native mouse gene identifiers, eliminating the need for ortholog mapping.