EntityFinder: 'EntityFinder'

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

Description

this function creates instances of the class EntityFinder

Usage

EntityFinder(input, dictionary, options = NA, outDir = tempdir(),
  multipleDocs = FALSE)

Arguments

input	the file, directory, or data frame with the text to annotate
dictionary	A dictionary of the type CMdictionary or the path to an already created Conceptmapper XML file
options	an object of class CMoptions. If NA, the default configuration will be set.
outDir	the directory where the annotated files will be stored
multipleDocs	TRUE when multiple documents are loaded from a single file with each row representing a document. The file should have two columns. The first for the unique document identifier and the second for the textual descriptions

Value

dataframe of annotations

Examples

obo <- system.file('extdata', 'sample.cs.obo', package='OnassisJavaLibs')
sample_dict <- CMdictionary(input=obo, outputDir=getwd(), synonymType='ALL')
myopts <- CMoptions()
paramValueIndex(myopts) <- 40
entities <- EntityFinder(input=readRDS(system.file('extdata', 'vignette_data', 'GEO_human_chip.rds', package='Onassis')), dictionary=sample_dict, options=myopts)

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