psygenet2r (version 1.2.0)

pantherGraphic: Query PsyGeNET for given genes and creates a representation in base of their panther-class

Description

Given a vector of genes of interest (or using a DataGeNET.Psy object), this function creates a representation of a the panther-class these genes belongs to.

Usage

pantherGraphic(x, database = "CURATED", score, verbose = FALSE, check = FALSE, hostMart = "www.ensembl.org", biomart = "ENSEMBL_MART_ENSEMBL")

Arguments

x

Vector of genes of interest of DataGeNET.Psy resulting of psyegnetDisease.

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

threshold to take into account a gene in the analysis

verbose

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

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

Value

A plot for a DataGeNET.Psy in terms of the panther-class.

Examples

d.alch <- pantherGraphic( c( "COMT", "CLOCK", "DRD3" ), "CURATED" )