get.bm: Make a Query to Biomart.

In convertid: Convert Gene IDs Between Each Other and Fetch Annotations from Biomart

Make a Query to Biomart.

Description

get.bm() is a user-friendly wrapper for getBM() from the biomaRt package with default settings for Human and Mouse. It sets all needed variables and performs the query.

Usage

get.bm(
  values,
  biom.data.set = c("human", "mouse"),
  biom.mart = c("ensembl", "mouse", "snp", "funcgen", "plants"),
  host = "https://www.ensembl.org",
  biom.filter = "ensembl_gene_id",
  biom.attributes = c("ensembl_gene_id", "hgnc_symbol", "description"),
  biom.cache = rappdirs::user_cache_dir("biomaRt"),
  use.cache = TRUE,
  verbose = FALSE
)

Arguments

values	character vector of ids to be converted.
biom.data.set	character of length one. Biomart data set to use. Defaults to 'human' (internally translated to "hsapiens_gene_ensembl" if biom.mart="ensembl").
biom.mart	character vector. Biomart to use (uses the first element of the vector), defaults to "ensembl".
host	character of length one. Host URL.
biom.filter	character of length one. Name of biomart filter, i.e., type of query ids, defaults to "ensembl_gene_id".
biom.attributes	character vector. Biomart attributes, i.e., type of desired result(s); make sure query id type is included!
biom.cache	character. Path name giving the location of the cache getBM() uses if use.cache=TRUE. Defaults to the value in the BIOMART_CACHE environment variable.
use.cache	(logical). Should getBM() use the cache? Defaults to TRUE as in the getBM() function and is passed on to that.
verbose	(logical). Should verbose output be written to the console? Defaults to FALSE.

Value

A data frame with the retrieved information.

Author(s)

Vidal Fey

See Also

getBM

Examples

## Not run: 
val <- c("ENSG00000111199", "ENSG00000134121", "ENSG00000176102", "ENSG00000171611")
bm <- get.bm(val)
bm

## End(Not run)

convertid documentation built on April 4, 2025, 1:01 a.m.