Fun.enrich_withFC: Fun.enrich_withFC

In chenweng1991/scMitoTracing: R package for Regulatory multi-omics with Deep Mitochondrial mutation profiling

Fun.enrich_withFC

Description

This function is to do GSEA enrichment analysis

Usage

Fun.enrich_withFC(
  markergenesList,
  All.genes = all.genes.refer,
  db = msig.db,
  qcutoff = 0.05,
  top = NULL
)

Arguments

markergenesList	is a list containing several elements each of which is a vector of gene names
All.genes	the background genes data(all.genes.refer)
db	=msig.db the term database to use, default is the msig.db; data(msig.db)
qcutoff=0.05	the term to show with q value lower than 0.05
top=NULL	pass a number to only show top # terms

Value

this will return a simple object with two elements, one is the table to show the significant terms , the other one shows the gene names involved significant terms

Examples

S7G.GSEA<-Fun.enrich_withFC(markergenesList=list(S7G=topS7G.genes),All.genes=all.genes.refer)

chenweng1991/scMitoTracing documentation built on July 2, 2024, 8:41 p.m.