UpdateSymbols: Update symbols using biomaRt

In grandR: Comprehensive Analysis of Nucleotide Conversion Sequencing Data

Update symbols using biomaRt

Description

If your input files only contained ENSEMBL ids, use this to add gene symbols!

Usage

UpdateSymbols(data, species = NULL, current.value = "ensembl_gene_id")

Arguments

data	a grandR object
species	the species the genes belong to (eg "Homo sapiens"); can be NULL, then the species is inferred from gene ids (see details)
current.value	What it the current value in the symbols field?

Details

If no species is given, a very simple automatic inference is done, which will only work when having human or mouse ENSEMBL identifiers as gene ids. If you need to specify species, it must be one of biomaRt::listDatasets(biomaRt::useMart("ensembl"))$dataset!

Current.value must be one of biomaRt::listAttributes(biomaRt::useMart("ensembl"))$name!

Value

a grandR object with updated symbol names

grandR documentation built on April 4, 2025, 2:27 a.m.