findEntities {Onassis} | R Documentation |
Method findEntities
This method finds concepts from a Conceptmapper Dictionary of type CMdictionary
in a given directory or in a single pipe separated file containing a named document in each row, with a specified configuration of type CMoptions
. This is a method of the EntityFinder-class
findEntities(object, inputDirOrFile, multipleDocs = FALSE, outDir = tempdir(), configOpt, cmDict) ## S4 method for signature ## 'EntityFinder,character,logical,character,CMoptions,CMdictionary' findEntities(object, inputDirOrFile, multipleDocs = FALSE, outDir = tempdir(), configOpt, cmDict)
object |
instance of the class EntityFinder |
inputDirOrFile |
the directory where the files to annotate are stored or the text file to annotate. A single file containing in each row sample names, the | symbol and the description of the sample is also allowed. |
multipleDocs |
TRUE if a single file containing different text sources has been given as inputDirOrFile. FALSE if each text is in a separate file. Defaults to FALSE |
outDir |
The directory where the Conceptmapper annotated files are stored. Default: the system tmp directory. |
configOpt |
Object of type CMoptions in which the parameters to run Conceptmapper are stored |
cmDict |
Instance of class |
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
obo <- system.file('extdata', 'sample.cs.obo', package='OnassisJavaLibs') dict <- CMdictionary(inputFileOrDb=obo, outputDir=getwd(), synonymType='ALL') opts <- CMoptions() ef <- new('EntityFinder') annotations <- findEntities(ef, system.file('extdata', 'test_samples', 'test_samples.txt', package='Onassis'), multipleDocs=TRUE, outDir=getwd(), configOpt=opts, cmDict=dict)