API for maize-genetics/rTASSEL
R Front-End for TASSEL

Global functions
.getTASSELClass	Source code
.onAttach	Source code
.onLoad	Source code
.tasselObjectConstructor	Source code
AssociationResults-class	Man page
AssociationResults-validity	Man page
AssociationResultsBLUE-class	Man page
AssociationResultsFast-class	Man page
AssociationResultsGLM-class	Man page
AssociationResultsMLM-class	Man page
PCAResults-class	Man page
PCAResults-validity	Man page
TasselDistanceMatrix-class	Man page
TasselGenotypePhenotype-class	Man page
as.matrix.TasselDistanceMatrix	Man page Source code
as.matrix.TasselGenotypePhenotype	Man page Source code
asTasselDistanceMatrix	Man page Source code
assocModelFitter	Man page Source code
associationType	Man page
associationType,AssociationResults-method	Man page
cell	Source code
checkForClassicId	Source code
checkForValidColumns	Source code
cleanUpMatrix	Source code
cleanUpTaxa	Source code
colnames,TasselDistanceMatrix-method	Man page
combineTasselGenotypePhenotype	Source code
concatenate	Man page Source code
createTree	Man page Source code
dim,TasselDistanceMatrix-method	Man page
distanceMatrix	Man page Source code
expectedQuantiles	Source code
exportGenotypeTable	Man page Source code
extractPhenotypeAttDf	Source code
filterByGRanges	Source code
filterGenotypeTableBySiteName	Man page Source code
filterGenotypeTableSites	Man page Source code
filterGenotypeTableTaxa	Man page Source code
generateQQData	Source code
genomicPrediction	Man page Source code
genomicRanges	Source code
getGenotypePhenotype	Source code
getGenotypeTable	Source code
getMinMaxPhysPositions	Source code
getMinMaxVarSites	Source code
getPhenotypeDF	Man page Source code
getPhenotypeTable	Source code
getPositionList	Source code
getSumExpFromGenotypeTable	Man page Source code
getTaxaIDs	Source code
getTaxaList	Source code
grToAesMappingDf	Source code
hClustPCAResults	Source code
imputeLDKNNi	Man page Source code
imputeNumeric	Man page Source code
intersectJoin	Man page Source code
kinshipMatrix	Man page Source code
ldCellRotater	Source code
ldJavaApp	Man page Source code
ldPlot	Man page Source code
linkageDiseq	Man page Source code
mds	Man page Source code
mergeGenotypeTables	Man page Source code
ncol,TasselDistanceMatrix-method	Man page
nrow,TasselDistanceMatrix-method	Man page
pca	Man page Source code
plotManhattan	Man page Source code
plotManhattanCore	Source code
plotManhattanCoreInteractive	Source code
plotManhattanQC	Man page Source code
plotManhattanQCCore	Source code
plotManhattanQCCoreInteractive	Source code
plotPCA	Man page Source code
plotPCACore	Source code
plotPCACoreInteractive	Source code
plotQQ	Man page Source code
plotQQCore	Source code
plotQQCoreInteractive	Source code
plotScree	Man page Source code
plotScreeCore	Source code
plotScreeCoreInteractive	Source code
positionList	Man page Source code
primeManhattanData	Source code
readGenotypePhenotype	Man page Source code
readGenotypeTableFromGigwa	Man page Source code
readGenotypeTableFromPath	Man page Source code
readPhenotypeFromDataFrame	Man page Source code
readPhenotypeFromPath	Man page Source code
readTasselDistanceMatrix	Man page Source code
reportNames	Man page
reportNames,AssociationResults-method	Man page
reportNames,PCAResults-method	Man page
returnReportElements	Source code
rotate	Source code
rownames,TasselDistanceMatrix-method	Man page
rtPaths	Man page
sampleDataFrame	Source code
seqDiversity	Man page Source code
show,AssociationResults-method	Man page
show,PCAResults-method	Man page
show,TasselDistanceMatrix-method	Man page
show,TasselGenotypePhenotype-method	Man page
siteSummary	Man page Source code
startLogger	Man page Source code
summaryDistance	Source code
tableReport	Man page
tableReport,AssociationResults-method	Man page
tableReport,AssociationResultsBLUE-method	Man page
tableReport,AssociationResultsFast-method	Man page
tableReport,AssociationResultsGLM-method	Man page
tableReport,AssociationResultsMLM-method	Man page
tableReport,PCAResults-method	Man page
tableReportList	Source code
tableReportListToAssociationResults	Source code
tableReportToDF	Source code
tasPhenoFilter	Source code
taxaList	Man page Source code
taxaSummary	Man page Source code
traitNames	Man page
traitNames,AssociationResults-method	Man page
traitValidityChecker	Source code
treeJavaApp	Man page Source code
truncate	Source code
unionJoin	Man page Source code