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NAMESPACE
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# Generated by roxygen2: do not edit by hand
S3method(as.matrix,TasselDistanceMatrix)
S3method(as.matrix,TasselGenotypePhenotype)
export(asTasselDistanceMatrix)
export(assocModelFitter)
export(associationType)
export(concatenate)
export(createTree)
export(distanceMatrix)
export(exportGenotypeTable)
export(filterGenotypeTableBySiteName)
export(filterGenotypeTableSites)
export(filterGenotypeTableTaxa)
export(genomicPrediction)
export(getPhenotypeDF)
export(getSumExpFromGenotypeTable)
export(imputeLDKNNi)
export(imputeNumeric)
export(intersectJoin)
export(kinshipMatrix)
export(ldJavaApp)
export(ldPlot)
export(linkageDiseq)
export(mds)
export(mergeGenotypeTables)
export(pca)
export(plotManhattan)
export(plotManhattanQC)
export(plotPCA)
export(plotQQ)
export(plotScree)
export(positionList)
export(readGenotypePhenotype)
export(readGenotypeTableFromGigwa)
export(readGenotypeTableFromPath)
export(readPhenotypeFromDataFrame)
export(readPhenotypeFromPath)
export(readTasselDistanceMatrix)
export(reportNames)
export(seqDiversity)
export(siteSummary)
export(startLogger)
export(tableReport)
export(taxaList)
export(taxaSummary)
export(traitNames)
export(treeJavaApp)
export(unionJoin)
exportClasses(AssociationResults)
exportClasses(AssociationResultsBLUE)
exportClasses(AssociationResultsFast)
exportClasses(AssociationResultsGLM)
exportClasses(AssociationResultsMLM)
exportClasses(PCAResults)
exportClasses(TasselDistanceMatrix)
exportClasses(TasselGenotypePhenotype)
exportMethods(associationType)
exportMethods(colnames)
exportMethods(ncol)
exportMethods(nrow)
exportMethods(reportNames)
exportMethods(rownames)
exportMethods(tableReport)
exportMethods(traitNames)
importFrom(GenomicRanges,end)
importFrom(GenomicRanges,seqnames)
importFrom(GenomicRanges,start)
importFrom(S4Vectors,DataFrame)
importFrom(SummarizedExperiment,SummarizedExperiment)
importFrom(ape,read.tree)
importFrom(methods,is)
importFrom(methods,new)
importFrom(rJava,"%instanceof%")
importFrom(rJava,.jarray)
importFrom(rJava,.jcall)
importFrom(rJava,.jchar)
importFrom(rJava,.jevalArray)
importFrom(rJava,.jinstanceof)
importFrom(rJava,.jnew)
importFrom(rJava,.jnull)
importFrom(rJava,.jrcall)
importFrom(rJava,.jstrVal)
importFrom(rJava,J)
importFrom(rJava,is.jnull)
importFrom(rJava,new)
importFrom(rlang,.data)
importFrom(utils,head)