convert.bm: Retrieve Additional Annotations from Biomart

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

Retrieve Additional Annotations from Biomart

Description

convert.bm() is a wrapper for get.bm() which in turn makes use of getBM() from the biomaRt package. It takes a matrix or data frame with the IDs to be converted in one column or as row names as input and returns a data frame with additional annotations after cleaning the fetched annotations and merging them with the input data frame.

Usage

convert.bm(
  dat,
  id = "ID",
  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,
  sym.col = "hgnc_symbol",
  rm.dups = FALSE,
  verbose = FALSE
)

Arguments

dat	matrix or data.frame. Matrix or data frame with the ids to be converted in a column or as row names.
id	character. Name of the column with the ids to be converted, special name "rownames" will use the row names.
biom.data.set	character of length one. Biomart data set to use.
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.
sym.col	character. Name of the column in the query result with gene symbols.
rm.dups	logical. Should duplicated input IDs (biom.filter) be removed from the result?
verbose	(logical). Should verbose output be written to the console? Defaults to FALSE.

Details

Wrapped around 'get.bm'.

Value

A data frame with the retrieved information.

Author(s)

Vidal Fey

See Also

getBM

Examples

## Not run: 
dat <- data.frame(ID=c("ENSG00000111199", "ENSG00000134121", "ENSG00000176102", "ENSG00000171611"))
bm <- convert.bm(dat)
bm

## End(Not run)

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