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

Description Usage Arguments Value Examples

Description

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

Usage

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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

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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.