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
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
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')
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
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Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(KEGGprofile)
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
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/KEGGprofile/find_enriched_pathway.Rd_%03d_medium.png", width=480, height=480)
> ### Name: find_enriched_pathway
> ### Title: find_enriched_pathway
> ### Aliases: find_enriched_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')
>
>
>
>
>
> dev.off()
null device
1
>
providing 
.