jaccardEstimation-methods: Calculation of the Jaccard Index between ideseases

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

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 = "ALL",
  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 '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.
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.

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.

Value

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

Examples

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

psygenet2r documentation built on Jan. 31, 2021, 2 a.m.