This is a wrapper around clusterProfiler::GSEA() to perform GSEA analysis for a given set of genes.
Usage
gsea_analysis(
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 denots 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()