• Added new function:
    • pca()
    • Allows for user to run PCA on rTASSEL objects containing a GenotypeTable object.
  • Added new function:
    • mds()
    • Allows for user to run MDS on TasselDistanceMatrix objects.
  • Enhancements:
    • New summary print output for TasselDistanceMatrix objects.
  • Added new TasselDistanceMatrix class
    • Specified function (kinshipMatrix() and distanceMatrix()) now return an object of type TasselDistanceMatrix.
    • Prevents console overload and freezing as seen with large distance matrix objects.
    • Now shows summary overview of matrix instead of Java object reference.
    • Generic functions colnames(), rownames(), ncol(), and nrow() will return relative information similar to how these operate with matrix type objects.
    • Primitive function as.matrix() now supersedes deprecated functions kinshipToRMatrix() and distanceToRMatrix().
    • Prior functions that take in a kinship object will now take in this new class.
  • Added new function:
  • Added new function:
    • asTasselDistanceMatrix()
    • Coerces a pairwise matrix (e.g. m x m dimensions) with the same column and row names of type matrix to an object of type TasselDistanceMatrix.
  • Added new function:
    • createTree()
    • interface to TASSEL’s tree creation methods
    • Allows for Neighbor_Joining and UPGMA methods
  • Added new function:
    • treeJavaApp()
    • wrapper for TASSEL’s interface to the Archaeopteryx Java tree Viewer
    • Implements same methods for tree creation as createTree()
  • Fix manhattanPlot() aesthetics:
    • Remove redundant marker labels from x-axis
    • Change x-axis label to SNP Positions
  • Added two new parameters to filterGenotypeTableSites()
    • removeMinorSNPStates: Boolean; removes minor SNP states.
    • removeSitesWithIndels: Boolean; removes sites with indels.
  • Added better descriptive error handling for filterGenotypeTableSites()
  • Fixed siteRangeFilterType parameter bug in filterGenotypeTableSites(). Now defaults to none when user does not specify filter type.
  • Added two new parameters to getSumExpFromGenotypeTable()
    • coerceDosageToInt: Returns raw byte dosage array instead of integer from Java.
    • verbose: Display console messages for large “memory-intensive” datasets.
  • Added functions to calculate linkage disequilibrium (LD)
  • Proposed LD functions:
  • Added write to file parameters for:
    • assocModelFitter()
  • Added p-value threshold parameters for:
    • assocModelFitter()
  • Added thread usage paramters for:
    • assocModelFitter()
  • Optimized table report to data frame generation
  • Added new filtration features for genotype tables via filterGenotypeTableSites()
    • parameters for variant sites
    • parameters for physical positions
    • filtration via chromsomome position files
    • filtration via BED file formats
  • Added error checks for catching C stack usage errors for the following functions:
    • filterGenotypeTableSites()
    • filterGenotypeTableTaxa()
  • Added NEWS file for tracking version updates.
  • Added new functions:
    • leaveOneFamilyOut()
    • genomicPredction()
  • Fixed a bug where tibbles when passed through readPhenotypeFromDataFrame(), would cause errors.