psygenet2r (version 1.2.0)

jaccardEstimation: Calculation of the Jaccard Index between ideseases

Description

This function is able to calculate the Jacard Index between: 1. muliple disases, 2. a set og genes and multiple diseases, 3. a set of genes and multiple main psychiatric disorders and 4. multiple diseases and multiple main psychiatric disorders.

Usage

jaccardEstimation(pDisease, sDisease, database = "CURATED", nboot = 100, ncores = 1, verbose = FALSE)

Arguments

pDisease

vector of diseases, vector of genes, vector of main psychiatric disorder.

sDisease

vector of diseases, vector of genes, vector of main psychiatric disorder. Only necessary when comparing genes vs. diseases, genes vs. main psychiatric disorders or diseases vs. main psychiatric disorders. To compare multiple diseases only use pDisease.

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'.

nboot

Number of iterations sued to compute the pvalue associted to the calculated Jaccard Index (default 100).

ncores

Number of cores used to calculate the pvalue associated to the computed Jaccard Index (default 1).

verbose

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

Value

An object of class JaccardIndexPsy with the computed calculation of the JaccardIndex.

Details

Warning: The main psychiatric disorders are understood as a single set of genes composed by the genes of all the diseases that the main psychiatric disorder cotains.

Examples

ji <- jaccardEstimation( c( "COMT", "CLOCK", "DRD3" ), "umls:C0005586", "CURATED" )