get.bm: 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
)

Value

A data frame with the retrieved information.

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.

Author

Vidal Fey

Examples

Run this code

if (FALSE) {
val <- c("ENSG00000111199", "ENSG00000134121", "ENSG00000176102", "ENSG00000171611")
bm <- get.bm(val)
bm
}