View source: R/data_generation.R
get_mgsigdb_gsets | R Documentation |
Retrieve Organism-specific MSigDB Gene Sets
get_mgsigdb_gsets(species = "Homo sapiens", collection, subcollection = NULL)
species |
species name, such as Homo sapiens, Mus musculus, etc.
See |
collection |
collection. i.e., H, C1, C2, C3, C4, C5, C6, C7. |
subcollection |
sub-collection, such as CGP, BP, etc. (default = NULL, i.e. list all gene sets in collection) |
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
Retrieves the MSigDB gene sets and returns a list containing 2 elements:
gene_setsA list containing the genes involved in each of the selected MSigDB gene sets
descriptionsA named vector containing the descriptions for each selected MSigDB gene set
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