Fun.enrich_withFC.pvalue — Fun.enrich

This function is to do GSEA enrichment analysis, to be updated

Usage

Fun.enrich_withFC.pvalue(
  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