get_biomart_mapping: Internal function for obtaining biomaRt mapping

In dnapath: Differential Network Analysis using Gene Pathways

Internal function for obtaining biomaRt mapping

Description

Internal function for obtaining biomaRt mapping

Usage

get_biomart_mapping(species, symbol_name, dir_save, verbose)

Arguments

species	The species to obtain a biomart dataset for. This should be an output from format_species_name.
symbol_name	The type of gene symbol to use. HGNC symbols are used by default (hgnc_symbol), unless species is "mmusculus", in which case MGI symbols are used (mgi_symbol).
dir_save	The directory to store annotation reference. Future calls to this function will use the stored annotations. This speeds up the operation and allows for reproducibility in the event that the biomaRt database is updated. Set to NULL to disable. By default, it uses a temporary directory to store files during the R session.
verbose	Set to FALSE to avoid messages.

Value

A data frame containing a mapping between entrezgene IDs and gene symbols.

dnapath documentation built on May 9, 2022, 9:05 a.m.