EntityFinder {Onassis} | R Documentation

## `EntityFinder`

### 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)

[Package Onassis version 1.6.1 Index]