annotateDF: 'annotateDF'

Description Usage Arguments Value Examples

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

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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

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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)

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