runHG: Run hypergeometric gene enrichment analysis.

In NMikolajewicz/scMiko: scRNAseq analysis functions. Developed using Seurat framework.

Run hypergeometric gene enrichment analysis.

Description

Run hypergeometric gene enrichment analysis.

Usage

runHG(
  gene.list,
  gene.universe,
  species,
  pathway.db = "Bader",
  n.workers = 16,
  my.pathway = NULL,
  my.pathway.representation = "ENTREZ",
  min.size = 2,
  max.size = 300,
  e2s = F,
  go.ontology = "BP",
  verbose = T
)

Arguments

gene.list	Named list of genesets to run enrichment on (symbol format).
gene.universe	Gene universe (symbol format)
species	Species. One of "Mm" (mouse) or "Hs" (human)
pathway.db	Name of databse to get annotation genelists from. Default is "Bader". See scMiko::getAnnotationPathways() for options.
n.workers	Number of workers for parallelization. Default is 16.
my.pathway	Named list of pathways, with each entry containing vector of Entrez IDs. Retrieved internally unless explicitly provided.
my.pathway.representation	If my.pathway is provided, species which format, options = "SYMBOL" or "ENTREZ". ENTREZ is Default.
min.size	min geneset size. Default is 2.
max.size	max geneset size. Default is 300.
e2s	entrez to symbol mapping (computationally demanding). Default False.
go.ontology	BP, MF or CC. Ignored if pathway.db != "GO".
verbose	Print progress. Default is TRUE.

Value

enrichment results

Author(s)

Nicholas Mikolajewicz

NMikolajewicz/scMiko documentation built on June 28, 2023, 1:41 p.m.