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Get auxiliary phenotype ontology maps

Source: R/get_aux_maps.R
get_aux_maps.Rd

Downloads and returns multiple phenotype dictionaries used for cross-referencing of terms, including UMLS, EFO, DO, and ICD10. The dataset comes as a list object, with two elements:

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

  • records - a list object with multiple lists/data.frames

Usage

get_aux_maps(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 4 rows 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

  • abbreviation - abbreviation used in column names of records

records - A list with the following elements:

  • umls - List with UMLS data dictionaries

  • do - Data frame with DO identifiers/names

  • efo - List with EFO data dictionaries

  • icd10 - Data frame with CUI to ICD10 cross-reference

Examples


if (FALSE) { # \dontrun{
library(phenOncoX)
oncology_terms <- get_aux_maps(cache_dir = tempdir())
} # }