Key2KEGGEnrich: Performe enrichment analysis based on KEGG pathway, plot...

In ppdragondw/Key2Enrich: R package of gene set enrichment analysis

Description

Performe enrichment analysis based on KEGG pathway, plot barplot of significantly enriched KEGG pathway, mapping genes on KEGG pathway image

Usage

Key2KEGGEnrich(inputSample, inputSpecies, adjustMethod, filterMethod,
  filterValue, ifbarplot, ifMapOnPath, type, imgWidth, imgHeight)

Arguments

inputSample	input formatted sample
inputSpecies	human, mouse, rat
adjustMethod	p.adjust.methods, c("holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none")
filterMethod	pValue or other character vector
filterValue	must by numeric, value from 0 to 1
ifbarplot	barplot or not, TRUE/FALSE
ifMapOnPath	pathway mapping or not, TRUE/FALSE
type	KEGG, Reactome, BP,MF,CC
imgWidth	the width of export file
imgHeight	the height of export file

Value

data in dataframe class with pValue, adjust pValue of significate KEGG pathway

Examples

data(inputSample)
inputSample<-as.data.frame(inputSample)
head(inputSample)
## Not run: 
KEGGSigMx<-Key2KEGGEnrich(inputSample,"mouse","fdr","fdr",0.05,TRUE,TRUE,"KEGG",15,20)

## End(Not run)

ppdragondw/Key2Enrich documentation built on May 29, 2019, 7:39 a.m.