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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show(<PHGDataSet>) - A PHGDataSet Class
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PHGDataSet() - PHGDataSet object constructor
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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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show(<PHGMetrics>) - A PHGMetrics Class
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PHGMetrics() - PHGMetrics object constructor
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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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`$`(<PHGMetrics>) - Access Elements of PHGMetrics Objects by Name
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.DollarNames(<PHGMetrics>) - Retrieve Names Matching a Pattern from PHGMetrics Objects
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filterRefRanges() - Filter data by reference range
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filterSamples() - Filter data by sample IDs
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`%T%` - User-defined function for pre-evaluated names in vectors
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hVcfFiles() - Return hVCF files
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host() - Return host data
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httProtocol() - Return protocol value
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initPhg() - Initialize JVM and add class path (for R&D purposes only)
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javaMemoryAddress() - Return
rJavareference object
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javaRefObj() - Return
rJavareference object
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metricsIds()`metricsIds<-`() - Return metrics table IDs
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metricsMetaData() - Return metric metadata
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metricsTable()`metricsTable<-`() - Return a metrics table
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numberOfChromosomes() - Return number of chromosomes
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numberOfHaplotypes() - Return number of haplotypes
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numberOfRefRanges() - Return number of reference ranges
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numberOfSamples() - Return number of samples
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phgType() - Return type of PHG connection
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plotDot() - Generate dot plots
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plotGvcf() - Generate GVCF plots
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plotHaploCounts() - Plot haplotype counts
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plotHaploDist() - Plot haplotype distribution
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port() - Return port value
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readHapIdMetaData() - Return haplotype ID metadata
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readHapIdPosMetaData() - Return haplotype ID positional metadata
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readHapIds() - Return haplotype IDs
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readPhgDataSet() - Return all hVCF data from a JVM graph
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readRefRanges() - Return reference ranges
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readSamples() - Return samples IDs
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seqnames(<PHGMetrics>) - Return all contig IDs from metrics object
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`seqnames<-`(<PHGMetrics>) - Set Sequence Names for PHGMetrics Object
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serverInfo() - Return server information