All functions

TasselDistanceMatrix-class

TasselDistanceMatrix Class

show(<TasselGenotypePhenotype>) show(<TasselDistanceMatrix>)

TasselGenotypePhenotype Class

as.matrix(<TasselDistanceMatrix>)

Coerce matrix from TasselDistanceMatrix class

asTasselDistanceMatrix()

Coerce matrix to TasselDistanceMatrix object

assocModelFitter()

R interface for TASSEL's association methods

colnames(<TasselDistanceMatrix>)

Column names

createTree()

R interface for TASSEL's tree creation methods

dim(<TasselDistanceMatrix>)

Get dimensions of TasselDistanceMatrix object

distanceMatrix()

Create a TASSEL distance matrix

exportGenotypeTable()

Export Genotype Table to Disk

filterGenotypeTableSites()

Filter genotype table by sites

filterGenotypeTableTaxa()

Filter genotype table by taxa

genomicPrediction()

R interface for TASSEL's genomic prediction capabilities

getPhenotypeDF()

Get an R/DataFrame phenotype data frame from TASSEL object

getSumExpFromGenotypeTable()

Create Summarized Experiment from a TASSEL Genotype Table

kinshipMatrix()

Create a TASSEL kinship matrix

ldJavaApp()

Linkage desequilibrium visualization application

ldPlot()

Linkage disequilibrium plot

linkageDiseq()

Calculate linkage disequilibrium from an rTASSEL genotype dataset.

manhattanPlot()

Create Manhattan plot from rTASSEL association output

ncol(<TasselDistanceMatrix>)

Number of columns

nrow(<TasselDistanceMatrix>)

Number of rows

readGenotypePhenotype()

Wrapper function of TasselGenotypePhenotype class for GenotypePhenotype combined data

readGenotypeTableFromPath()

Wrapper function of TasselGenotypePhenotype class for genotype data

readPhenotypeFromDataFrame()

Wrapper function of TasselGenotypePhenotype class for phenotype data from an R data frame

readPhenotypeFromPath()

Wrapper function of TasselGenotypePhenotype class for phenotype data from a path.

readTasselDistanceMatrix()

read TASSEL distance matrix object from file

rownames(<TasselDistanceMatrix>)

Row names

startLogger()

Start TASSEL logging information

treeJavaApp()

R interface for Archaeopteryx interactive tree viewer