GetGeneIds: Get different gene IDs.

In mevers/RNAModR: Functional Analysis of RNA Modifications

Description

Get different gene IDs for mapping between different gene annotations (Ensembl, Entrez, etc.). See 'Details'. This is a low-level function that is being called from BuildTx.

Usage

GetGeneIds(txdb)

Arguments

txdb	A TxDb object.

Details

The function extracts the genome assembly version from the TxDb object, and loads the suitable genome wide annotation package. For example, if TxDb is based on "hg38", the function loads org.Hs.eg.db. Various IDs (Ensembl, gene symbols) are extracted from the annotation package by mapping RefSeq IDs from TxDb via mapIds from the AnnotationDbi package. Please note that column entries are not necessarily unique: For example, two different Ensembl IDs might have the same Entrez ID. The return object is a data.frame with the following columns:

• tx_refseq: RefSeq Accession number; these entries are unique and refer to the mRNA transcript

• gene_entrez: Entrez gene ID

• gene_symbol: Gene symbol

• gene_ensembl: Ensembl gene ID

• gene_name: Gene name

Note that mapping between gene IDs is a many-to-many mapping process. For example, different transcript RefSeq IDs can belong to the same gene. Which transcripts are associated with which gene depends in turn on the gene reference system (RefSeq, Ensembl, etc.). On top of that, the same transcript may have >1 location in the reference genome: NM_000451 (EntrezID 6473) is annotated on chromosomes X and Y, NM_001001418 (EntrezID 414060) has two loci on chr17.

Value

A DataFrame. See 'Details'.

Author(s)

Maurits Evers, [e-mail]

mevers/RNAModR documentation built on Nov. 17, 2019, 9:11 a.m.