convert2EntrezID: Convert other common IDs to entrez gene ID.

In LihuaJulieZhu/ChIPpeakAnno: Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments or any experiments resulted in large number of chromosome ranges

Description

Convert other common IDs such as ensemble gene id, gene symbol, refseq id to entrez gene ID leveraging organism annotation dataset. For example, org.Hs.eg.db is the dataset from orgs.Hs.eg.db package for human, while org.Mm.eg.db is the dataset from the org.Mm.eg.db package for mouse.

Usage

convert2EntrezID(IDs, orgAnn, ID_type = "ensembl_gene_id")

Arguments

IDs	a vector of IDs such as ensembl gene ids
orgAnn	organism annotation dataset such as org.Hs.eg.db
ID_type	type of ID: can be ensemble_gene_id, gene_symbol or refseq_id

Value

vector of entrez ids

Author(s)

Lihua Julie Zhu

Examples

ensemblIDs = c("ENSG00000115956", "ENSG00000071082", "ENSG00000071054",
 "ENSG00000115594", "ENSG00000115594", "ENSG00000115598", "ENSG00000170417")
library(org.Hs.eg.db)
entrezIDs = convert2EntrezID(IDs=ensemblIDs, orgAnn="org.Hs.eg.db",
 ID_type="ensembl_gene_id")

LihuaJulieZhu/ChIPpeakAnno documentation built on Aug. 5, 2020, 12:02 a.m.