SDA.GO_Enrichment: Perform Gene Ontology Enrichment Analysis on SDA Components

In eisascience/scCustFx: single-cell custom fxs Package

Perform Gene Ontology Enrichment Analysis on SDA Components

Description

This function conducts Gene Ontology (GO) enrichment analysis on specified components from Single-cell Data Analysis (SDA) results. It supports analysis in positive, negative, or both directions and allows specifying the number of top genes to consider. The function utilizes 'clusterProfiler' for the enrichment analysis and is capable of handling different organism databases.

Usage

SDA.GO_Enrichment(
  sdaResults,
  components,
  orgDb = "org.Hs.eg.db",
  geneNumber = 100,
  direction = "Both"
)

Arguments

sdaResults	A list containing SDA results, expected to include a 'loadings' element with components and gene loadings.
components	A numeric vector indicating which components from the SDA results to analyze.
orgDb	A character string specifying the Bioconductor organism annotation package to use for the enrichment analysis. Default is "org.Hs.eg.db" for human. Other examples include "org.Mm.eg.db" for mouse and "org.Mmu.eg.db" for rhesus macaque.
geneNumber	An integer specifying the number of top genes to consider for enrichment analysis in each component and direction. Default is 100.
direction	A character string indicating the direction of gene loading to consider for the analysis. Can be "Pos" for positive, "Neg" for negative, or "Both" for both directions. Default is "Both".

Value

A list where each element corresponds to a component and direction analyzed, containing the results of the GO enrichment analysis. Results include enrichment scores, gene ratios, background ratios, and odds ratios among others.

eisascience/scCustFx documentation built on June 2, 2025, 3:59 a.m.