phecap_generate_dictionary_file: Generate a Dictionary File for Note Parsing

In PheCAP: High-Throughput Phenotyping with EHR using a Common Automated Pipeline

Description

Given a list of CUIs, connect to the UMLS database stored in MySQL, extract CUIs and associated terms, and write a dictionary file for use in note parsing.

Usage

phecap_generate_dictionary_file(
  cui_list, dict_file,
  user = "username", password = "password",
  host = "localhost", dbname = "umls", ...)

Arguments

cui_list	a character vector consisting of CUIs of interest.
dict_file	a character scalar for the path to the dictionary file that will be generated.
user	a character scalar for the username for database connection; passed to RMySQL::dbConnect as it is.
password	a character scalar for the password for database connection; passed to RMySQL::dbConnect as it is.
host	a character scalar for the host (or URL) for database connection; passed to RMySQL::dbConnect as it is.
dbname	a character scalar for the database name for database connection; passed to RMySQL::dbConnect as it is.
...	Other arguments passed to RMySQL::dbConnect as they are.

Value

The dictionary will be written to the location given by dict_file. Return the dictionary invisibly.

PheCAP documentation built on Sept. 17, 2020, 5:07 p.m.