annotateDF: 'annotateDF'

In Onassis: OnASSIs Ontology Annotation and Semantic SImilarity software

Description

Method to find concepts from a Conceptmapper Dictionary of type CMdictionary contained in a given data frame, with a specified configuration of type CMoptions. This is a method of the EntityFinder-class

Usage

annotateDF(object, descr_df, outDir = tempdir(), configOpt, cmDict)

## S4 method for signature 'EntityFinder,data.frame,character,CMoptions'
annotateDF(object,
  descr_df, outDir = tempdir(), configOpt, cmDict)

Arguments

object	Instance of class EntityFinder-class
descr_df	the table of text to annotate. The data frame should have identifiers in the first column and descriptions or text in the rest of the columns.
outDir	the output directory
configOpt	instance of class CMoptions-class
cmDict	Object of type CMdictionary-class containing the reference to a previously created Conceptmapper dictionary. Alternatively the path to a Conceptmapper xml file can be passed.

Value

A data frame of annotations containing the sample name, the id of the OBO concept, the corresponding name, the part of the text containing the annotation

Examples

obo <- system.file('extdata', 'sample.cs.obo', package='OnassisJavaLibs')
dict <- CMdictionary(inputFileOrDb=obo, outputDir=getwd(), synonymType='ALL')
opts <- CMoptions()
ef <- new('EntityFinder')
methylation <- readRDS(system.file('extdata', 'vignette_data',
'GEOmethylation.rds', package='Onassis'))
annotations <- annotateDF(ef, methylation[1:10, ], getwd(), opts, dict)

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