psygenetGene: Query PsyGeNET for given gene(s) and generates an `DataGeNET.Psy`

Description

Given the name of one or multiple gene and retrives their information from PsyGeNET and creates an object of type DataGeNET.Psy.

Usage

psygenetGene(gene, database = "CURATED", score = c(">", 0), check = FALSE, hostMart = "www.ensembl.org", biomart = "ENSEMBL_MART_ENSEMBL", verbose = FALSE, warnings = TRUE)

Arguments

gene

Name or vector of names (that can be both code or symbol) to specific genes from PsyGeNET. The genes non existing in PsyGeNET will be removed from the output.

database

Name of the database that will be queried. It can take the values 'MODELS' to use Comparative Toxigenomics Database, data from mouse and rat; 'GAD' to use Genetic Association Database; 'CTD' to use Comparative Toxigenomics Database, data from human; 'PsyCUR' to use Psychiatric disorders Gene association manually curated; 'CURATED' to use Human, manually curated databases (PsyCUR and CTD); or 'ALL' to use all these databases. Default 'CURATED'.

score

A vector with two elements: 1) character with greather '>' or with lower '<'< code=""> meaing greather or equal and lower or

check

By default FALSE. Change it to TRUE to validate the genes to biomart.

hostMart

The URL of Biomart to be used.

biomart

By default 'ENSEMBL_MART_ENSEMBL'. The mart of biomart used to check genes

verbose

By default FALSE. Change it to TRUE to get a on-time log from the function.

warnings

By default TRUE. Change it to FALSE to not see the warnings.

Value

An object of class DataGeNET.Psy

Examples

Run this code

d.alch <- psygenetGene( "ALDH2", "CURATED" )

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