v0.9.33

• Fixed typo in plotPCA() error message
• Add new function filterGenotypeTableBySiteName():
  • Filters genotype tables using literal marker names/IDs
• Add new function mergeGenotypeTables():
  • Merges multiple genotype tables by site values

v0.9.32

• Updated tableReport() method dispatch for all AssociationResults
  objects:
  • Will now return default statistics output for all association results
    when running tableReport(assocObj) where assocObj is an object
    of type AssociationResults
• Removed HDF5 file export support
• Improved logic support for plotPCA()
• Added new PCAResults class
  • Allows for more controlled access of data and simplified downstream
    functions for end users
• Add new function plotScree():
  • Generates quick scree plots from PCAResults objects
• Add new function plotPCA():
  • Generates quick PCA plots from PCAResults objects
  • Allows for grouping from generated hierarchical clustering or grouping
    from metadata via the metadata parameter and subsequent mCol
    parameters.
• Added new AssociationResults class
  • Allows for more controlled access of data and simplified downstream
    functions for end users
• Added new function plotManhattan():
  • Supercedes older Manhattan plotting methods to work with new
    AssociationResults class.
• Added new function plotQQ():
  • Plotting function for QQ results from AssociationResults class
• Added new function plotManhattanQC():
  • Plotting function and QC method for zoomed in regions of interest
    across genome
• Prior 3 functions also include interactive component that wraps
  ggplot2 objects with PlotlyJS components

v0.9.29

• Added genotype table summary methods:
  • positionList()
  • taxaSummary()
  • siteSummary()
• TasselGenotypePhenotype objects containing genotype table data can now
  be coerced into R matrix objects using the function as.matrix()
  • This will return a taxa x site matrix where taxa is the number of rows and
    sites is the number of columns.
• Added generalized join methods:
  • intersectJoin()
  • unionJoin()
  • Joins phenotype data data based on taxa ID - similar to the TASSEL API
• Added read method for importing GIGWA data through QBMS:
  • readGenotypeTableFromGigwa()

v0.9.28

• Fixed log4j warning issue
  • This removes log4j warning messages when the startLogger() function
    is called.
• Removed useRef parameter from getSumExpFromGenotypeTable() function.
  • This is now automatically detected from the file input.
  • This fixes ref/alt allele vs major/minor allele encoding issues.
• Added Journal of Open Source Software citation for the rTASSEL package.
  • For citation information, use utils::citation("rTASSEL")
• Added data object, rtPaths
  • Includes paths to external toy data for rTASSEL

v0.9.27

• No significant updates in this version. This version is virtually identical
  to 0.9.26 and is for linking to Zenodo for archival purposes.

v0.9.26

• Bug fixes:
  • Fixed r2 parameter bug in ldPlot()
  • Fixed space bugs in certain column names of data frame objects.
    _ values now replace spaces.
  • Fixed show() method for TasselDistanceMatrix objects.
• Add new function:
  • seqDiversity()
  • Calculates diversity basic diversity metrics on genetic data.

v0.9.23

• 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:
  • readTasselDistanceMatrix()
  • Allows for user to read in delimited distance matrix stored in a flat
    file.
• 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()