Function reference • rTASSEL

All functions

TasselDistanceMatrix-class: TasselDistanceMatrix Class

show(<TasselGenotypePhenotype>) show(<TasselDistanceMatrix>): TasselGenotypePhenotype Class

as.matrix(<TasselDistanceMatrix>): Coerce matrix from TasselDistanceMatrix class

as.matrix(<TasselGenotypePhenotype>): Coerce genotype table to R matrix

asTasselDistanceMatrix(): Coerce matrix to TasselDistanceMatrix object

assocModelFitter(): R interface for TASSEL's association methods

colnames(<TasselDistanceMatrix>): Column names

concatenate(): Concatenate phenotype tables

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

imputeLDKNNi(): LD KNNi imputation

imputeNumeric(): Imputation methods in Numerical Transformations

intersectJoin(): Intersect join phenotype tables

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

mds(): Run MDS on TasselDistanceMatrix objects

ncol(<TasselDistanceMatrix>): Number of columns

nrow(<TasselDistanceMatrix>): Number of rows

pca(): Run PCA on Genotype Table

positionList(): Get position list metadata from genotype table

readGenotypePhenotype(): Wrapper function of TasselGenotypePhenotype class for GenotypePhenotype combined data

readGenotypeTableFromGigwa(): Read genotype data from GIGWA using QBMS

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

rtPaths: Paths to TASSEL toy data

seqDiversity(): Calculate sequence diversity

siteSummary(): Get site summary of genotype table

startLogger(): Start TASSEL logging information

taxaList(): Get list of taxa from TASSEL data

taxaSummary(): Get taxa summary of genotype table

treeJavaApp(): R interface for Archaeopteryx interactive tree viewer

unionJoin(): Union join phenotype tables