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Get human gene aliases from NCBI

Source: R/get_alias.R
get_alias.Rd

Downloads and returns a dataset that indicate ambiguous and unambiguous gene aliases/synonyms for human genes. Gene aliases with less than three characters have been ignored, and a few custom aliases have been added (source = custom). The dataset comes as a list object, with two elements:

  • metadata - a data frame with metadata regarding annotation resources used

  • records - a list with gene aliases indicating ambiguous/ non-ambiguous state

Usage

get_alias(cache_dir = NA, force_download = FALSE)

Arguments

cache_dir

Local directory for data download

force_download

Logical indicating if local cache should be overwritten (set to TRUE to re-download if file exists in cache)

Value

metadata - A data frame with 1 row and 6 columns:

  • source - gene annotation source

  • annotation_data - type of annotations used

  • url - URL of annotation resource

  • citation - publication to cite for annotation source (citation; PMID)

  • version - version used/datestamp

  • abbreviation - abbreviation used in column names of records

records - A data frame with 177,916 rows and 5 columns:

  • alias - gene alias/synonym

  • symbol - primary symbol

  • entrezgene - Entrez gene identifier

  • n_primary_map - number of primary symbols linked to the alias

  • ambiguous - logical indicating if alias is ambiguous or not

  • source - source for gene synonyms (NCBI, custom)

Examples

if (FALSE) { # \dontrun{
library(geneOncoX)
gene_alias <- get_alias(cache_dir = tempdir())
} # }