run_hypergeometric_gsea: Compute enriched gene sets among significant genes in a cell...

In scITD: Single-Cell Interpretable Tensor Decomposition

Compute enriched gene sets among significant genes in a cell type for a factor using hypergeometric test

Description

Compute enriched gene sets among significant genes in a cell type for a factor using hypergeometric test

Usage

run_hypergeometric_gsea(
  container,
  factor_select,
  ctype,
  up_down,
  thresh = 0.05,
  min_gs_size = 15,
  max_gs_size = 500,
  db_use = "GO"
)

Arguments

container	environment Project container that stores sub-containers for each cell type as well as results and plots from all analyses
factor_select	numeric The factor of interest
ctype	character The cell type of interest
up_down	character Either "up" to compute enrichment among the significant positive loading genes or "down" to compute enrichment among the significant negative loading genes.
thresh	numeric Pvalue significance threshold. Used as cutoff for calling genes as significant to use for enrichment tests. (default=0.05)
min_gs_size	numeric Minimum gene set size (default=15)
max_gs_size	numeric Maximum gene set size (default=500)
db_use	character The database of gene sets to use. Database options include "GO", "Reactome", "KEGG", and "BioCarta". More than one database can be used. (default="GO")

Value

A vector of adjusted p-values for enrichment of gene sets in the significant genes of a given cell type in a given factor.

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