get_biomart_metadb: get_biomart_metadb

In snplinkage: Single Nucleotide Polymorphisms Linkage Disequilibrium Visualizations

get_biomart_metadb

Description

To query gene names of SNPs, it is necessary to retrieve two objects using biomaRt::useMart. First, the object required to map SNP rs identifiers to ENSEMBL identifiers. Second, the object required to map ENSEMBL identifiers to common gene names. The function returns a list of two slots named snpmart and ensembl corresponding to each one, respectively. Once obtained it is saved to a local file.

Usage

get_biomart_metadb(
  filepath = extdata_filepath("bmart_meta.rds"),
  host = "https://grch37.ensembl.org"
)

Arguments

filepath	Path to save the biomaRt objects
host	BiomaRt Ensembl host, by default https://grch37.ensembl.org

Value

List of slots snpmart and ensembl as detailed above

snplinkage documentation built on May 4, 2023, 9:09 a.m.