ens2sym: Convert Ensembl IDs to gene symbols.

In vari-bbc/bbcRNA: Bulk RNA-seq workflow for VAI BBC

Description

Convert Ensembl IDs to gene symbols.

Usage

ens2sym(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.

Details

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

• Symbols that match multiple Ensembl IDs will be resolved by concatenating the Ensembl ID and the gene symbol. Uses scater::uniquifyFeatureNames.

• Genes with multiple possible symbols will be labelled as Ensembl ID.

• Genes absent from OrgDb/Biomart will be labelled as Ensembl ID.

Value

A BbcSE object.

vari-bbc/bbcRNA documentation built on Nov. 10, 2020, 11:09 p.m.