download_ctd_dise: Function to download diseases available in CTDbase

In CTDquerier: Package for CTDbase data query, visualization and downstream analysis

Description

This function download the "Disease vocabulary" file (CTD_diseases.tsv.gz) from http://ctdbase.org/downloads.

Usage

download_ctd_dise(filename = "CTD_diseases.tsv.gz", mode = "auto",
  verbose = FALSE)

Arguments

filename	(default "CTD_diseases.tsv.gz") Name of the file in the local system.
mode	(default "auto") Mode passed to download.file.
verbose	(default FALSE) If set to TRUE is shows relevant information of each step.

Details

The field included in the file (CTD_diseases.tsv.gz) are:

1. DiseaseName

2. DiseaseID (MeSH or OMIM identifier)

3. Definition

4. AltDiseaseIDs (alternative identifiers; '|'-delimited list)

5. ParentIDs (identifiers of the parent terms; '|'-delimited list)

6. TreeNumbers (identifiers of the disease's nodes; '|'-delimited list)

7. ParentTreeNumbers (identifiers of the parent nodes; '|'-delimited list)

8. Synonyms ('|'-delimited list)

9. SlimMappings (MEDIC-Slim mappings; '|'-delimited list)

Value

Passed name into filename argument if it could be download 1 otherwise. download_ctd_dise() file.exists( "CTD_diseases.tsv.gz" )

CTDquerier documentation built on Oct. 31, 2019, 2:57 a.m.