get_module_enr: Identify gene sets that are enriched within specified gene...

In scITD: Single-Cell Interpretable Tensor Decomposition

Identify gene sets that are enriched within specified gene co-regulatory modules. Uses a hypergeometric test for over-representation. Used in plot_multi_module_enr().

Description

Identify gene sets that are enriched within specified gene co-regulatory modules. Uses a hypergeometric test for over-representation. Used in plot_multi_module_enr().

Usage

get_module_enr(container, ctype, mod_select, db_use = "GO", adjust_pval = TRUE)

Arguments

container	environment Project container that stores sub-containers for each cell type as well as results and plots from all analyses
ctype	character The name of cell type for the cell type module to test
mod_select	numeric The module number for the cell type module to test
db_use	character The database of gene sets to use. Database options include "GO", "Reactome", "KEGG", "BioCarta", "Hallmark", "TF", and "immuno". More than one database can be used. (default="GO")
adjust_pval	logical Set to TRUE to apply FDR correction (default=TRUE)

Value

A vector of p-values for the tested gene sets.

scITD documentation built on Sept. 8, 2023, 5:11 p.m.