EntityFinder: 'EntityFinder'

Description Usage Arguments Value Examples

View source: R/AllConstructors.R

Description

this function creates instances of the class EntityFinder

Usage

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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

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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)

Onassis documentation built on Nov. 8, 2020, 8:18 p.m.