Epilepsy Ontology Similarities

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Documentation for package ‘epos’ version 0.1.0

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calcCosine Calculate the cosine similarity metric for two lists a and b
calcDice Calculate the dice similarity metric for two lists a and b
calcJaccard Calculate the jaccard coefficient for two lists a and b
cosine Calculate cosine similarity metric
createBaseTable Create the final resulting data frame
createDashVectorForATC Creates a vector with an X at each position where a drug from the druglist matches the ATC class list slatc
createJaccardPlotDBMeSH Creates the plot for all jaccard coefficients amongst the three epilepsy ontologies
createJaccardPlotMeSHFive Creates the plot for all jaccard coefficients amongst the three epilepsy ontologies
createNeuroTable Main function to call everything and produce the results
createTanimotoBaseline Creates the plot for all jaccard coefficients amongst the three epilepsy ontologies
dice Calculate dice similarity metric
doFullPlot Does the full plot on one page
filterApprovedDrugs Filter a given list of drug names for having an ATC code, if not they are dropped
filterNeuroDrugs Filter a given list of drug names for having an ATC code starting with N indicating to be a drug for the Nervous System
genDictListFromRawFreq Clears object that was loaded from harddrive into a list of terms sorted by frequency
jaccard Calculate jaccard similarity metric for two sets a and b
rawDrugBankCoOcEPILONT List of frequency named by drug terms that co-occur with the EPILONT ontology in the corpus of LIVIVO.
rawDrugBankCoOcEpSO List of frequency named by drug terms that co-occur with the EpSO ontology in the corpus of LIVIVO.
rawDrugBankCoOcESSO List of frequency named by drug terms that co-occur with the ESSO ontology in the corpus of LIVIVO.
readAtcMapIntoHashMapAtcCodesAtcNames Processes the input file db-atc.map to form a HashMap containing the drug names with ATC codes
readAtcMapIntoHashMapDrugNamesAtcCodes Processes the input file db-atc.map to form a HashMap containing the drug names with ATC codes
readSecondLevelATC Read the second level ATC classes from the file drugbankatc-secondlevel.map