getEnrichedPATH: Obtain enriched PATH that near the peaks

Description

Obtain enriched PATH that are near the peaks using path package such as reactome.db and path mapping package such as org.Hs.db.eg to obtain the path annotation and using hypergeometric test (phyper) and multtest package for adjusting p-values

Usage

getEnrichedPATH(annotatedPeak, orgAnn, pathAnn,  feature_id_type="ensembl_gene_id",  maxP=0.01, minPATHterm=10, multiAdjMethod=NULL)

Arguments

annotatedPeak

GRanges such as data(annotatedPeak) or a vector of feature IDs

orgAnn

organism annotation package such as org.Hs.eg.db for human and org.Mm.eg.db for mouse, org.Dm.eg.db for fly, org.Rn.eg.db for rat, org.Sc.eg.db for yeast and org.Dr.eg.db for zebrafish

pathAnn

pathway annotation package such as KEGG.db, reactome.db

feature_id_type

the feature type in annotatedPeakRanges such as ensembl_gene_id, refseq_id, gene_symbol or entrez_id

maxP

maximum p-value to be considered to be significant

minPATHterm

minimum count in a genome for a path to be included

multiAdjMethod

multiple testing procedures, for details, see mt.rawp2adjp in multtest package

Value

path.id: KEGG PATH ID
EntrezID: Entrez ID
count.InDataset: count of this PATH in this dataset
count.InGenome: count of this PATH in the genome
pvalue: pvalue from the hypergeometric test
totaltermInDataset: count of all PATH in this dataset
totaltermInGenome: count of all PATH in the genome
PATH: PATH name

References

Johnson, N. L., Kotz, S., and Kemp, A. W. (1992) Univariate Discrete Distributions, Second Edition. New York: Wiley

Examples

Run this code

if (interactive()) {
data(annotatedPeak)
library(org.Hs.eg.db)
library(reactome.db)
enriched.PATH = getEnrichedPATH(annotatedPeak, orgAnn="org.Hs.eg.db", 
                 pathAnn="reactome.db", maxP=0.01,
                 minPATHterm=10, multiAdjMethod=NULL)
 head(enriched.PATH)
}