API for maize-genetics/rPHG
R front-end for the practical haplotype graph

Global functions
.onAttach	Source code
.onLoad	Source code
HaplotypeGraph-class	Man page
HaplotypeGraph-validity	Man page
PHGCon-class	Man page
PHGCon-validity	Man page
PHGDataSet-class	Man page
PHGLocalCon	Man page Source code
PHGLocalCon-class	Man page
PHGLocalCon-validity	Man page
PHGMethod	Man page Source code
PHGMethod-class	Man page
PHGMethod-validity	Man page
PHGServerCon	Man page Source code
PHGServerCon-class	Man page
PHGServerCon-validity	Man page
amUrlContextStringBuilder	Source code
brapiEndpointExists	Source code
brapiURL	Man page
brapiURL,PHGServerCon-method	Man page
brapiVersion	Man page
brapiVersion,PHGServerCon-method	Man page
buildHaplotypeGraph	Man page Source code
calcMutualInfo	Man page
calcMutualInfo,PHGDataSet-method	Man page
calcMutualInfoFromPHGDataSet	Source code
configCatcher	Source code
configFilePath	Man page
configFilePath,PHGLocalCon-method	Man page
createConfigFile	Source code
dbName	Man page
dbName,PHGLocalCon-method	Man page
dbType	Man page
dbType,PHGLocalCon-method	Man page
descriptionStringToList	Source code
getProperty	Source code
graphFromHaplotypes	Source code
graphFromPaths	Source code
gvcfMetrics	Man page Source code
hapIdsFromGraphObj	Source code
hapIdsFromLocal	Source code
hapIdsFromSever	Source code
host	Man page
host,PHGCon-method	Man page
httProtocol	Man page
httProtocol,PHGServerCon-method	Man page
httpResp	Source code
isDemo	Man page
isDemo,PHGMethod-method	Man page
javaMemoryAddress	Man page
javaMemoryAddress,HaplotypeGraph-method	Man page
javaRefObj	Man page
javaRefObj,HaplotypeGraph-method	Man page
json2tibble	Man page Source code
methodTableFromLocal	Source code
methodTableFromServer	Source code
mutualInfoPair	Source code
nHaploPerRefRangeFromPHGDataSet	Source code
numHaploPerRefRange	Man page
numHaploPerRefRange,PHGDataSet-method	Man page
numberOfChromosomes	Man page
numberOfChromosomes,HaplotypeGraph-method	Man page
numberOfNodes	Man page
numberOfNodes,HaplotypeGraph-method	Man page
numberOfRefRanges	Man page
numberOfRefRanges,HaplotypeGraph-method	Man page
numberOfTaxa	Man page
numberOfTaxa,HaplotypeGraph-method	Man page
parseConfigFile	Source code
parseJSON	Source code
pathsForMethod	Source code
phgConObj	Man page
phgConObj,PHGMethod-method	Man page
phgDataSetFromGraphObj	Source code
phgDataSetFromLocal	Source code
phgDataSetFromServer	Source code
phgMethodId	Man page
phgMethodId,HaplotypeGraph-method	Man page
phgMethodId,PHGMethod-method	Man page
phgMethodType	Man page
phgMethodType,HaplotypeGraph-method	Man page
phgType	Man page
phgType,PHGCon-method	Man page
plotDot	Man page Source code
plotGraph	Man page
plotGraph,PHGDataSet-method	Man page
plotGraphCore	Source code
plotMutualInfo	Man page
plotMutualInfo,PHGDataSet-method	Man page
plotMutualInfoFromPHGDataSet	Source code
port	Man page
port,PHGServerCon-method	Man page
readHaplotypeIds	Man page
readHaplotypeIds,HaplotypeGraph-method	Man page
readHaplotypeIds,PHGMethod-method	Man page
readPHGDataSet	Man page
readPHGDataSet,HaplotypeGraph-method	Man page
readPHGDataSet,PHGMethod-method	Man page
readRefRanges	Man page
readRefRanges,HaplotypeGraph-method	Man page
readRefRanges,PHGMethod-method	Man page
readSamples	Man page
readSamples,HaplotypeGraph-method	Man page
readSamples,PHGMethod-method	Man page
refRangesFromGraphObj	Source code
refRangesFromLocal	Source code
refRangesFromServer	Source code
samplesFromGraphObj	Source code
samplesFromLocal	Source code
samplesFromServer	Source code
serverInfo	Man page
serverInfo,PHGServerCon-method	Man page
show	Man page
show,HaplotypeGraph-method	Man page
show,PHGLocalCon-method	Man page
show,PHGMethod-method	Man page
show,PHGServerCon-method	Man page
showPHGMethods	Man page
showPHGMethods,PHGLocalCon-method	Man page
showPHGMethods,PHGServerCon-method	Man page
startLogger	Man page Source code
tableReportToDF	Source code
taxaByNode	Man page
taxaByNode,PHGDataSet-method	Man page
taxaByNodeCore	Source code