psygenetGeneSentences: Query PsyGeNET for given gene(s) and extract the pmids...

In aGutierrezSacristan/psygenet2r: psygenet2r - An R package for querying PsyGeNET and to perform comorbidity studies in psychiatric disorders

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 = "ALL", 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 'psycur15' to use data validated by experts for first release of PsyGeNET; 'psycur16' to use data validated by experts for second release of PsyGeNET; or 'ALL' to use both databases. Default 'ALL'.
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")

aGutierrezSacristan/psygenet2r documentation built on Jan. 18, 2024, 4:06 a.m.