Epilepsy Ontologies' Similarities

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Documentation for package ‘epos’ version 1.1

Help Pages

calcCosine Calculate the cosine similarity metric for two lists a and b
calcDice Calculate the dice similarity metric for two lists a and b
calcDSEA Calculate dsea scores of one list in comparison to reference list
calcEnrichment Calculate enrichment of one list in comparison to reference list
calcJaccard Calculate the jaccard coefficient for two lists a and b
cosine Calculate cosine similarity metric
createBaseTable Main function to call everything and produce the results
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 Create the final resulting data frame
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
drawVenn4 Create quad Venn Diagramm for overlapping concepts between EpSO, ESSO, EPILONT and EPISEM
drawVenn4Doc Create quintuple Venn Diagramm for shared documents with co-occurrences of drug names between EpSO, ESSO, EPILONT and EPISEM
drawVenn4DrugDoc Create quad Venn Diagramm for shared documents with co-occurrences of drug names between EpSO, ESSO, EPILONT and EPISEM
drawVenn4Syn Create quad Venn Diagramm for shared synonyms between EpSO, ESSO, EPILONT and EPISEM
drawVenn5 Create quintuple Venn Diagramm for overlapping concepts between EpSO, ESSO, EPILONT, EPISEM and FENICS
drawVenn5Doc Create quintuple Venn Diagramm for shared documents between EpSO, ESSO, EPILONT, EPISEM and FENICS
drawVenn5DrugDoc Create quintuple Venn Diagramm for shared documents with co-occurrences of drug names between EpSO, ESSO, EPILONT, EPISEM and FENICS
drawVenn5Syn Create quintuple Venn Diagramm for shared synonyms between EpSO, ESSO, EPILONT, EPISEM and FENICS
drawVennGrid Create plot_grid from multiple plots
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
getRefAll Retrieve the list of drugs from the union of all reference lists
getTermMatrix Receives a sorted hashmap with found entities from a dictionary
jaccard Calculate jaccard similarity metric for two sets a and b
plotDSEA Plotting functions for DSEA lists
plotEnrichment Plotting functions for enrichment lists
printTop10Drugs Print Top 10 Drugs
rawDrugNamesCoOcEPILONT List drug terms with their frequency co-occurring with terms from the EPILONT ontology in publications since 2015 from the BioASQ 2020 corpus.
rawDrugNamesCoOcEPISEM List drug terms with their frequency co-occurring with terms from the EPISEM ontology in publications since 2015 from the BioASQ 2020 corpus.
rawDrugNamesCoOcEpSO List drug terms with their frequency co-occurring with terms from the EpSO ontology in publications since 2015 from the BioASQ 2020 corpus.
rawDrugNamesCoOcESSO List drug terms with their frequency co-occurring with terms from the ESSO ontology in publications since 2015 from the BioASQ 2020 corpus.
rawDrugNamesCoOcFENICS List drug terms with their frequency co-occurring with terms from the FENICS ontology in publications from the BioASQ 2020 corpus.
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 atc-secondlevel.map
sortTableByRefMatches Sort table by scoring for each row