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

Description Usage Arguments Details Value Author(s) Examples

View source: R/pathwayKS.R

pathway enrichment analysis using KS test

1 2	pathwayKS(wholePvalues, wholeName, fdr = 1.1, database = NULL, pathSizeMin = 15, pathSizeMax = 200)

`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

pathway enrichment analysis using KS exaxt test

pathway enrichment result table

Caleb

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