annotateDF {Onassis} | R Documentation |
annotateDF
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
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)
object |
Instance of 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 |
cmDict |
Object of type |
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') methylation <- readRDS(system.file('extdata', 'vignette_data', 'GEOmethylation.rds', package='Onassis')) annotations <- annotateDF(ef, methylation[1:10, ], getwd(), opts, dict)