Similarity: 'Similarity'

In Onassis: OnASSIs Ontology Annotation and Semantic SImilarity software

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)

Onassis documentation built on Nov. 8, 2020, 8:18 p.m.