enrichMsigDB: Perform over representation analysis (ORA) against Molecular...

In cparsania/parcutils: Utility Functions To Deal Day To Day Bioinformatics Tasks.

Perform over representation analysis (ORA) against Molecular Signature Database (MsigDB) .

Description

Perform over representation analysis (ORA) against Molecular Signature Database (MsigDB) .

Usage

enrichMsigDB(
  gene_list,
  from_type = "SYMBOL",
  orgdb = org.Mm.eg.db::org.Mm.eg.db,
  msigdb_category = "H",
  msigdb_subcategory = NULL,
  species = "Mus musculus",
  background = NULL,
  col_genetype = "GENETYPE",
  feature_type = "protein-coding",
  ...
)

Arguments

gene_list	a character vector denoting valid gene names.
from_type	a string, default SYMBOL, denoting the type of input gene_list (e.g SYMBOL, ENTREZID).
orgdb	an object of the class OrgDB. Default org.Mm.eg.db::org.Mm.eg.db.
msigdb_category	a character string, default "H", denoting one of the nine catagories of geneList given in the msigdb. Possible values are: "H","C1","C2","C3","C4","C5","C6","C7", and "C8". Values will be passed to the argument category of the function msigdbr::msigdbr().
msigdb_subcategory	a character string, default NULL, denoting MSigDB sub-collection abbreviation, such as CGP or BP. Values will be passed to the argument subcategory of the function msigdbr::msigdbr().
species	a character string denoting name of the species. Default "Mus musculus". Possible values can be found via the function msigdbr::msigdbr_species(). Values will be passed to the argument species of the function msigdbr::msigdbr().
background	NULL (default) or a character vector. If NULL, all features filtered by feature_type will be selected as background. In case of character vector, values will be used as it is for background set. In case of user provided background set it is assumed that id type is same as queried genes_list (i.e. from_type). NOTE: In both scenarios values obtained from MSigDB category database will always remain as a part of background set.
col_genetype	A string denoting a column name to filter feature_type.Valid only if the argument background is NULL.
feature_type	A string denoting a value to filter the column mentioned by the argument col_genetype.Valid only if the argument background is NULL.
...	Other parameters to pass clusterProfiler::enricher().

Value

Enrichment results.

cparsania/parcutils documentation built on Oct. 27, 2024, 4:55 a.m.