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

1
2
3
find_enriched_pathway(gene, species = "hsa", returned_pvalue = 0.01,
  returned_adjpvalue = 0.05, returned_genenumber = 5,
  download_latest = FALSE, refGene = NULL)

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.

refGene

the names of genes used as reference. If not provided, all genes in KEGG database will be used.

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

1
2
3
4
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 Nov. 17, 2017, 12:28 p.m.