gene_per_term: For the results from 'compareClusterResult' object

In Yutong441/TBdev: Infer a Trophoblast Developmental Trajectory

Description

This function will print all the GO/KEGG/Reactome terms that match the requested keyword or phrases with their p values. It will optionally return a list of all the genes corresponding to the matches terms

Usage

gene_per_term(
  xx,
  term,
  organism_db,
  category_col = "Description",
  return_val = F
)

Arguments

xx	a compareClusterResult object
term	a keyword that matches the term of interest
organism_db	which organism database, for example, org.Hs.eg.db
category_col	which column in x that has the terms
return_val	whether to return the gene names

Examples

KG <- modules::use ('KEGG_path.R')
library (GOSemSim)
d <- godata('org.Hs.eg.db', ont="BP")
kk <- KG$compare_cluster_enrichment (markers, d, enrich_area='KEGG')
path_val <- KG$gene_per_term (kk, 'JAK-STAT', org.Hs.eg.db, return_val=T)

Yutong441/TBdev documentation built on Dec. 18, 2021, 8:22 p.m.