jaccardEstimation {psygenet2r} | R Documentation

## 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 = "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" )

[Package psygenet2r version 1.22.5 Index]