hyperGtest_jimmy: Hypergeometric Tests for GO/KEGG test by jimmy

In jmzeng1314/humanid: gene id annotation

Description

Given GeneID2Path,Path2GeneID,diff_gene,universeGeneIds, this function will compute Hypergeometric Tests for each path (GO/KEGG), It can't hold on the structure of the GO graph, just a simple path .

Usage

hyperGtest_jimmy(GeneID2Path = GeneID2kegg_list,
  Path2GeneID = kegg2GeneID_list,
  diff_gene = sample(unique(hgu95av2_id$gene_id), 500),
  universeGeneIds = unique(hgu95av2_id$gene_id))

Arguments

GeneID2Path	a list which one entrez gene id to multiple pathway id,default:GeneID2kegg_list
Path2GeneID	a list which one pathway id to multiple entrezgene id,default:kegg2GeneID_list
diff_gene	a vector which contain the significantly DEG list, abouth 500~1000 genes(entrez gene id ),default:sample(unique(hgu95av2_id$gene_id),500)
universeGeneIds	a vector which contain the backgroud gene list,probably 20,000 genes , default:unique(hgu95av2_id$gene_id)

Value

a data.frame, each row is a Hypergeometric Tests result for each pathway .

Examples

#' hyperGtest_jimmy(),hyperGtest_jimmy()

jmzeng1314/humanid documentation built on May 19, 2019, 2:57 p.m.