sim {Onassis} | R Documentation |
sim
This method computes the similarities of the entities annotated in a object fo class Onassis-class
.
sim(onassis = NA, ...) ## S4 method for signature 'Onassis' sim(onassis, iconf = "sanchez", pairconf = "lin", groupconf = "bma")
onassis |
instance of class |
... |
Optional parameters |
iconf |
the information content measure see |
pairconf |
the pairwse measure to compute semantic similarity between single concepts. See |
groupconf |
the groupwise measure to compute semantic similarity between groups of concepts. See |
an instance of Onassis-class
with computed similarities
geo_chip <- readRDS(system.file('extdata', 'vignette_data', 'GEO_human_chip.rds', package='Onassis')) obo <- system.file('extdata', 'sample.cs.obo', package='OnassisJavaLibs') onassis_results <- annotate(geo_chip, 'OBO', dictionary=obo) entities <- entities(onassis_results) entities(onassis_results) <- entities[sample(nrow(entities), 30),] onassis_results <- sim(onassis_results)