find_enriched_pathway: find_enriched_pathway

In KEGGprofile: An annotation and visualization package for multi-types and multi-groups expression data in KEGG pathway

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

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

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')

Example output

KEGG.db contains mappings based on older data because the original
  resource was removed from the the public domain before the most
  recent update was produced. This package should now be considered
  deprecated and future versions of Bioconductor may not have it
  available.  Users who want more current data are encouraged to look
  at the KEGGREST or reactome.db packages

KEGGprofile documentation built on Nov. 8, 2020, 6:13 p.m.