Convert Ensembl IDs to Entrez IDs for gene enrichment analyses.

Convert Ensembl IDs to Entrez IDs for gene enrichment analyses.

ens2entrez(x, orgdb, BMdataset = "")

Arguments

x

A BbcSE object.
orgdb

A OrgDb object. Download the annotations for your species from 'http://bioconductor.org/packages/release/BiocViews.html#___OrgDb'. Only used if BMdataset="".
BMdataset

character. The name of the BM dataset you want to use. Try to use 'bbcRNA::searchBM("species_name")' to find the appropriate dataset if needed.

Value

A BbcSE object.

Details

Entrez IDs with more than one Ensembl ID match are determined only from genes present in the BbcSE object, so be sure it is unfiltered.

  • Entrez IDs that match multiple Ensembl IDs are NA

  • The first Entrez ID will be returned for genes with multiple possible Entrez IDs.

  • Genes with no Entrez ID or absent from the database will be NA.