Similarity {Onassis} | R Documentation |
Similarity
this constructr initializes the Similarity class to compute the similarity between couple of terms, couple of samples, or group of terms
Similarity(ontology, termlist1, termlist2, annotatedtab = NA, icConf = "seco", pairConf = "lin", groupConf = "ui")
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 |
Measure of the similarity bewtween the concepts passed as input
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)