query_ctd_chem: Function to query CTDbase using chemical terminology (...

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

Description

This function cheks for CTDbase gene vocabulary and query CTDbase for each one, downloading chemica-genes interactions, associated diseases, associated KEGG pathways and associated GO terms.

Usage

query_ctd_chem(terms, filename = "CTD_chemicals.tsv.gz", mode = "auto",
  max.distance = 10, verbose = FALSE)

Arguments

terms	Character vector with the chemicals used in the query.
filename	(default "CTD_chemicals.tsv.gz") Name of the file to store the CTDbase chemicals vocabilary.
mode	(default "auto") Mode passed to download.file.
max.distance	(default 10) Maximum distance allowed between a given element in terms argument and a possible match in CTDbase.
verbose	(default FALSE) If set to TRUE is shows relevant information of each step.

Value

An object of class CTDdata.

Examples

rst <- query_ctd_chem( terms = c( "Iron", "Air Pollutants" ), verbose = TRUE )

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