convertid (version 0.2.1)

convert.bm: 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
)

Value

A data frame with the retrieved information.

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.

Author

Vidal Fey

Details

Wrapped around `get.bm`.

See Also

getBM

Examples

if (FALSE) {
dat <- data.frame(ID=c("ENSG00000111199", "ENSG00000134121", "ENSG00000176102", "ENSG00000171611"))
bm <- convert.bm(dat)
bm
}