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

In isglobal-brge/CTDquerier: Package for CTDbase data query, visualization and downstream analysis

Function to query CTDbase using chemical terminology ( Chemical Name )

Description

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

Usage

query_ctd_chem(terms, max.distance = 10, ask = FALSE, verbose = FALSE)

Arguments

terms	Character vector with the chemicals used in the query.
max.distance	(default 10) Maximum distance allowed between a given element in terms argument and a possible match in CTDbase.
ask	(default TRUE) If TRUE it asks the the persistent location must be used to save the vocabulary if it was not downloaded previously.
verbose	(default FALSE) If set to TRUE is shows relevant information of each step.

Value

An object of class CTDdata.

Examples

# Example in a tryCatch, since we are performing a connection to a server we might
# get a refused connection due to a server rejection. Evaluate the recieved HTTP 
# message to understand if the server is not available or if your IP adress is temporarly restricted
rst <- tryCatch({query_ctd_chem( terms = c( "Iron", "Air Pollutants" ), verbose = TRUE )}, error = function(w){NULL})

isglobal-brge/CTDquerier documentation built on Oct. 6, 2022, 1:18 p.m.