find_enriched_pathway: find_enriched_pathway

Description Usage Arguments Details Value Examples

View source: R/KEGG_function.R

Description

The function will map the genes in KEGG pathway database, and then hypergegeometric tests would be used to estimate the significance of enrichment for each pathway

Usage

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find_enriched_pathway(gene, species = "hsa", returned_pvalue = 0.01,
  returned_adjpvalue = 0.05, returned_genenumber = 5,
  download_latest = FALSE)

Arguments

gene

a numeric matrix

species

the species id in KEGG database, 'hsa' means human, 'mmu' means mouse, 'rno' means rat, etc

returned_pvalue

the minimum p value for enriched pathways

returned_adjpvalue

the minimum adjusted p value for enriched pathways

returned_genenumber

the minimum number of annotated genes for enriched pathways

download_latest

logical. Indicate if the function will download the latest pathway/gene link from KEGG website. As the KEGG.db package was not updated for a long time due to the KEGG policy change, we provided this parameter so that the users could get the latest KEGG database.

Details

Only the pathways with p value <= returned_pvalue in hypergegeometric tests and number of annotated genes >= returned_genenumber would be taken as enriched and returned.

Value

a list with two parts

name stastic

description a matirx containing the pathway IDs of enriched pathways, and their names, p values, number of annotated genes

name detail

description a list with the genes annotated for each pathway

Examples

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data(pho_sites_count)
#the 300 genes with most phospholation sites quantified
genes<-names(rev(sort(pho_sites_count[,1]))[1:300])
pho_KEGGresult<-find_enriched_pathway(genes,species='hsa')

KEGGprofile documentation built on May 31, 2017, 2:51 p.m.