psygenet2r (version 1.2.0)

psygenetGeneSentences: Query PsyGeNET for given gene(s) and extract the pmids sentences that report a gene-disease asssociation.

Description

Given a gene or a gene list, retrives the pmids and sentences for each gene-disease association from PsyGeNET and creates an object of type DataGeNET.Psy.

Usage

psygenetGeneSentences(geneList, database = "CURATED", verbose = FALSE)

Arguments

geneList

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'.

verbose

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

Value

An object of class DataGeNET.Psy

Examples

genesOfInterest <- c("PECR", "ADH1C", "CAST", "ERAP1", "PPP2R2B",
                     "ESR1", "GATA4", "CDH13")
psyGeneSen <- psygenetGeneSentences( geneList = genesOfInterest,
                                     database = "ALL")