samplesim: 'samplesim'

In eugeniaeueu/Onassis: OnASSIs Ontology Annotation and Semantic SImilarity software

Description

This method computes the semantic similarity between two named samples annotated with a group of ontolgy terms belonging to the same ontology

Usage

samplesim(object, sample1, sample2, annotated_df)

## S4 method for signature 'Similarity,character,character,data.frame'
samplesim(object,
  sample1, sample2, annotated_df)

Arguments

object	instance of class Similarity-class
sample1	A sample ID with its annotations available in a data frame
sample2	A sample ID with its annotations available in a data frame
annotated_df	data frame with annotations obtained using entityFinder. The data frame should have at least a column named 'sample_id' with the sample identifier and a column named 'term_url' with the URL of the ontology terms annotating the sample. The ontology terms must belong to the ontology loaded in the Similarity class.

Value

The semantic similarity between the samples sample1 and sample2

Examples

sim <- new('Similarity')

pairwiseConfig(sim) <- listSimilarities()$pairwiseMeasures[9]
groupConfig(sim) <- listSimilarities()$groupwiseMeasures[3]
ef <- new('EntityFinder')
opts <- CMoptions()
obo <- system.file('extdata', 'sample.cs.obo', package='OnassisJavaLibs')
ontology(sim) <- obo
sample_dict <- CMdictionary(inputFileOrDb=obo, outputDir=getwd(), synonymType='ALL')
sra_chip_seq <- readRDS(system.file('extdata', 'vignette_data', 'GEO_human_chip.rds',
  package='Onassis'))
chipseq_dict_annot <- EntityFinder(sra_chip_seq[1:20,c('sample_accession', 'title',
 'experiment_attribute', 'sample_attribute', 'description')], dictionary=sample_dict,
  options=opts)
s <- samplesim(sim, as.character(as.vector(chipseq_dict_annot$sample_id[1])),
as.character(as.vector(chipseq_dict_annot$sample_id[7])) , chipseq_dict_annot)

eugeniaeueu/Onassis documentation built on March 9, 2020, 8:17 a.m.