collapse {Onassis} | R Documentation |
collapse
This method collapses semantic states in an Onassis object.
collapse(onassis = NA, simil_thresh) ## S4 method for signature 'Onassis' collapse(onassis = NA, simil_thresh)
onassis |
instance of class |
simil_thresh |
the semantic similarity threshold to use to merge similar semantic sets |
a new object of class Onassis-class
with collapsed annotations for the entities and a new similarity matrix of similarities between newly created semantic sets
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), 15),] onassis_results <- sim(onassis_results) collapsed_onassis <- collapse(onassis_results, 0.9)