Function reference • rTASSEL

All functions

show(<AssociationResults>): AssociationResults Class

AssociationResults-validity: AssociationResults validation

AssociationResultsBLUE-class: AssociationResultsBLUE Class

AssociationResultsFast-class: AssociationResultsFast Class

AssociationResultsGLM-class: AssociationResultsGLM Class

AssociationResultsMLM-class: AssociationResultsMLM Class

show(<PCAResults>): PCAResults Class

PCAResults-validity: PCAResults validation

show(<TasselDistanceMatrix>): TasselDistanceMatrix Class

show(<TasselGenotypePhenotype>): 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

associationType(): Return GWAS association type

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

filterGenotypeTableBySiteName(): Filter genotype table by site IDs

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.

mds(): Run MDS on TasselDistanceMatrix objects

mergeGenotypeTables(): Merge genotype tables

ncol(<TasselDistanceMatrix>): Number of columns

nrow(<TasselDistanceMatrix>): Number of rows

pca(): Run PCA on Genotype Table

plotManhattan(): Create a Manhattan plot from rTASSEL association output

plotManhattanQC(): Create a QC Manhattan plots from rTASSEL association output

plotPCA(): Generate PCA plot

plotQQ(): Create a QQ plot from rTASSEL association output

plotScree(): Generate scree plots

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

reportNames() traitNames(<AssociationResults>): Return report names

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

tableReport(): Return selected table report

taxaList(): Get list of taxa from TASSEL data

taxaSummary(): Get taxa summary of genotype table

traitNames(): Return trait names

treeJavaApp(): R interface for Archaeopteryx interactive tree viewer

unionJoin(): Union join phenotype tables