getEnrichedPATH: Obtain enriched PATH that near the peaks

In jianhong/ChIPpeakAnno: Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments, or any experiments that result in large number of genomic interval data

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,
  subGroupComparison = 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 (deprecated), reactome.db, KEGGREST
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
subGroupComparison	A logical vector to split the peaks into two groups. The enrichment analysis will compare the over-present GO terms in TRUE group and FALSE group separately. The analysis will split into two steps: 1. enrichment analysis for TRUE group by hypergeometric test; 2. enrichment analysis for TRUE over FALSE group by Fisher's Exact test for the enriched GO terms. To keep the output same format, if you want to compare FALSE vs TRUE, please repeat the analysis by inverting the parameter. Default is NULL.

Value

A dataframe of enriched path with the following variables.

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

Author(s)

Jianhong Ou, Kai Hu

References

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

See Also

phyper, hyperGtest

Examples

if (interactive()||Sys.getenv("USER")=="jianhongou") {
data(annotatedPeak)
library(org.Hs.eg.db)
library(reactome.db)
enriched.PATH = getEnrichedPATH(annotatedPeak, orgAnn="org.Hs.eg.db",
                 feature_id_type="ensembl_gene_id",
                 pathAnn="reactome.db", maxP=0.01,
                 minPATHterm=10, multiAdjMethod=NULL)
 head(enriched.PATH)
 enrichedKEGG = getEnrichedPATH(annotatedPeak, orgAnn="org.Hs.eg.db",
                 feature_id_type="ensembl_gene_id",
                 pathAnn="KEGGREST", maxP=0.01,
                 minPATHterm=10, multiAdjMethod=NULL)
 enrichmentPlot(enrichedKEGG)
}

jianhong/ChIPpeakAnno documentation built on Feb. 2, 2024, 3:26 p.m.