pathwayFisher: pathway analysis

In Caleb-Huo/genomicLibrary: commonly used genomic functions in R

Description

pathway enrichment analysis using Fisher exaxt test

Usage

pathwayFisher(significant, whole, fdr = 1.1, database = NULL,
  pathSizeMin = 15, pathSizeMax = 200)

Arguments

significant	a vector of hit genes
whole	a vector of background genes
fdr	desired FDR cutoff. Only pathways passed the FDR cutoff will survive
database	a list of pathway database, each list element contains a vector of genes

Details

pathway enrichment analysis using Fisher exaxt test

Value

pathway enrichment result table

Author(s)

Caleb

Examples

whole <- letters
significant <- letters[1:5]
database <- list(d1=letters[2:20],d2=letters[5:26])
pathwayFisher(significant, whole, database=database)

Caleb-Huo/genomicLibrary documentation built on June 4, 2020, 3:54 a.m.