Get mapped Entrez Gene IDs from CpG probe names

Share:

Description

Given a set of CpG probe names and optionally all the CpG sites tested, this function outputs a list containing the mapped Entrez Gene IDs as well as the numbers of probes per gene, and a vector indicating significance.

Usage

1
getMappedEntrezIDs(sig.cpg, all.cpg = NULL, array.type)

Arguments

sig.cpg

character vector of significant CpG sites used for testing gene set enrichment

all.cpg

character vector of all CpG sites tested. Defaults to all CpG sites on the array.

array.type

the Illumina methylation array used. Options are "450K" or "EPIC".

Details

This function is used by the gene set testing functions gometh and gsameth. It maps the significant CpG probe names to Entrez Gene IDs, as well as all the CpG sites tested. It also calculated the numbers of probes for gene.

Genes associated with each CpG site are obtained from the annotation package IlluminaHumanMethylation450kanno.ilmn12.hg19 if the array type is "450K". For the EPIC array, the annotation package IlluminaHumanMethylationEPICanno.ilm10b2.hg19 is used.

Value

A list with the following elements

sig.eg

mapped Entrez Gene IDs for the significant probes

universe

mapped Entrez Gene IDs for all probes on the array, or for all the CpG probes tested.

freq

table output with numbers of probes associated with each gene

de

a vector of ones and zeroes of the same length of universe indicating which genes in the universe are significantly differentially methylated.

Author(s)

Belinda Phipson

See Also

gometh,gsameth

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
library(IlluminaHumanMethylation450kanno.ilmn12.hg19)
library(org.Hs.eg.db)
library(limma)
ann <- getAnnotation(IlluminaHumanMethylation450kanno.ilmn12.hg19)

# Randomly select 1000 CpGs to be significantly differentially methylated
sigcpgs <- sample(rownames(ann),1000,replace=FALSE)

# All CpG sites tested
allcpgs <- rownames(ann)

mappedEz <- getMappedEntrezIDs(sigcpgs,allcpgs,array.type="450K")
mappedEz$sig.eg[1:10]
mappedEz$universe[1:10]
mappedEz$freq[1:10]
mappedEz$de[1:10]