Similarity {Onassis} | R Documentation

## `Similarity`

### Description

this constructr initializes the Similarity class to compute the similarity between couple of terms, couple of samples, or group of terms

### Usage

    Similarity(ontology, termlist1, termlist2, annotatedtab = NA,
      icConf = "seco", pairConf = "lin", groupConf = "ui")

### Arguments

`ontology` | The ontology file to create the DAG to compute similarities
`termlist1` | The single concept or vector of concepts in the first set or the name of a sample if annotatedtab contains an annotated table
`termlist2` | The single concept or vector of concepts in the second set or the name of a sample if annotatedtab contains an annotated table
`annotatedtab` | The table of annotation of samples or entities
`icConf` | the information content configuration
`pairConf` | the pairwise configuration
`groupConf` | the groupwise configuration

### Value

Measure of the similarity bewtween the concepts passed as input

### Examples

    obo <- system.file('extdata', 'sample.cs.obo', package='OnassisJavaLibs')
    sample_dict <- CMdictionary(input=obo, outputDir=getwd(), synonymType='ALL')
    myopts <- CMoptions(paramValueIndex=40)
    term_list1 <- c('http://purl.obolibrary.org/obo/CL_0000000', 'http://purl.obolibrary.org/obo/CL_0000236')
    term_list2 <- c('http://purl.obolibrary.org/obo/CL_0000542')
    sim <- Similarity(obo, term_list1, term_list2)

[Package Onassis version 1.4.5 Index]