hyperGTest_multiple: Hypergeometric Tests for a list of geneSets

In jmzeng1314/geneSet:

Description

It'll do Hypergeometric Tests for a list of geneSets, such as KEGG database. And we need 3 parameters, first is this_geneSet which contains all of the genes in this geneSet. Then is choose_geneIds,which probably is the significantly differently expression genes. Last is the backgroud_geneIds, which should be all of the genes which have been detected by microarray or RNA-seq, and so on . The N is the size of backgroud_geneIds The n is the size of choose_geneIds The M is the size of intersect(this_geneSet,backgroud_geneIds) The K is the size of intersect(this_geneSet,choose_geneIds) The exp_count is n*M/N The OddsRatio is k/exp_count The p is the statistic P value for this Hypergeometric Tests

Usage

hyperGTest_multiple(geneSet_list = list(set1 = sample(1:100, 10), set2 =
  sample(1:100, 10)), choose_geneIds = sample(1:100, 20),
  backgroud_geneIds = 1:100)

Arguments

geneSet_list	A list which contains all of the vector for each geneSet.
choose_geneIds	A vector which contains all of gene which defined by user, probably significantly differently expression genes.
backgroud_geneIds	A vector which contains all of the genes have been detected by microarray or RNA-seq, and so on

Value

a data.frame which has 8 columns:geneSet_name,N,n,M,k,exp_count,OddsRatio,p)

Examples

hyperGTest_multiple()

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