gseMsigDB: Perform gene set enrichment analysis against Molecular...

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

Perform gene set enrichment analysis against Molecular Signature Database (MSigDB).

Description

This is a wrapper around clusterProfiler::GSEA() to perform GSEA analysis against MsigDB.

Usage

gseMsigDB(
  gene_list,
  from_type = "SYMBOL",
  orgdb = org.Mm.eg.db::org.Mm.eg.db,
  msigdb_category = "H",
  species = "Mus musculus",
  ...
)

Arguments

gene_list	a named numeric vector. Values in the vector will be used to rank the genes in GSEA analysis. Values can be normalised expression, log2FC, test statistics etc. Vector names denote gene names.
from_type	a character string, default "SYMBOL", denotes type of gene identifier. Possible values could be one of those available as keys of OrgDB object.
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".
species	a character string denoting name of the species. Default "Mus musculus". Possible values can be found via the function msigdbr::msigdbr_species().
...	other arguments to be passed to clusterProfiler::GSEA().

Value

an output of clusterProfiler::GSEA().

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