pathwayKS: pathway analysis

Description Usage Arguments Details Value Author(s) Examples

View source: R/pathwayKS.R

Description

pathway enrichment analysis using KS test

Usage

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pathwayKS(wholePvalues, wholeName, fdr = 1.1, database = NULL,
  pathSizeMin = 15, pathSizeMax = 200)

Arguments

wholePvalues

a vector of p values for all genes

wholeName

a vector of all genes symbols

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 KS exaxt test

Value

pathway enrichment result table

Author(s)

Caleb

Examples

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wholePvalues <- rnorm(26)
wholeName <- letters[1:26]
database <- list(d1=letters[2:20],d2=letters[5:26])
pathwayKS(wholePvalues, wholeName, database=database, fdr=1)

Caleb-Huo/genomicLibrary documentation built on May 6, 2019, 9:27 a.m.