Package index
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show(<HaplotypeGraph>) - A HaplotypeGraph Class
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HaplotypeGraph-validity - HaplotypeGraph validation
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PHGCon-class - A PHGCon Class
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PHGCon-validity - PHGCon validation
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PHGDataSet-class - A PHGDataSet class
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show(<PHGLocalCon>) - A PHGLocalCon Class
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PHGLocalCon-validity - PHGLocalCon validation
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PHGLocalCon() - Helper function to construct a
PHGLocalConobject
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PHGMethod-class - A PHGMethod Class
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PHGMethod-validity - PHGMethod validation
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PHGMethod() - Helper function to construct PHGMethod object
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show(<PHGServerCon>) - An PHGServerCon Class
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PHGServerCon-validity - BrAPI connection validation
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PHGServerCon() - PHGServerCon object constructor
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brapiURL() - Return URL path
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brapiVersion() - Return BrAPI version ID
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buildHaplotypeGraph() - Helper function to build HaplotypeGraph object
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calcMutualInfo() - Calculate mutual information for a given PHG data set
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configFilePath() - Return file path of configuration file
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dbName() - Return name of DB
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dbType() - Return type of DB
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gvcfMetrics() - Generate metrics for GVCF data
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host() - Return host data
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httProtocol() - Return protocol value
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isDemo() - Return demo state
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javaMemoryAddress() - Return
rJavareference object
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javaRefObj() - Return
rJavareference object
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json2tibble() - JSON to tibble converter
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numHaploPerRefRange() - Return number of haplotypes per reference range
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numberOfChromosomes() - Return number of chromosomes
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numberOfNodes() - Return number of nodes
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numberOfRefRanges() - Return number of reference ranges
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numberOfTaxa() - Return number of taxa
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phgConObj() - Return a PHG connection object
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phgMethodId() - Return method ID
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phgMethodType() - Return method ID type
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phgType() - Return type of PHG connection
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plotDot() - Generate dot plot from Anchor files
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plotGraph() - Plot a graph object
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plotMutualInfo() - Plot mutual information
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port() - Return port value
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readHaplotypeIds() - Return haplotype IDs
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readPHGDataSet() - Return a PHGDataSet
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readRefRanges() - Return reference ranges
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readSamples() - Return samples IDs
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serverInfo() - Return server information
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show(<PHGMethod>) - Show method for PHGMethod objects
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showPHGMethods() - Return available PHG methods
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startLogger() - Start PHG logging information
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taxaByNode() - Return taxa info for haplotype IDs