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Changelog

Source: NEWS.md

rTASSEL 0.12.0

  • Fixed Codecov upload in CI by replacing covr::codecov() with the official codecov/codecov-action GitHub Action uploader

rTASSEL 0.11.0

  • Add fixes to possible issues related to ggplot2 v4.0
  • Bug fixes for filterGenotypeTableSites():
    • Fixed error “missing value where TRUE/FALSE needed” when filtering by position with matching start/end chromosomes and NULL position values
    • Added input validation for negative startSite and endSite values
    • Added input validation for negative startPos and endPos values
  • Removed bundled JAR files from inst/java/ to reduce package size
  • Added setupTASSEL() function to download TASSEL JARs from Maven Central and cache them locally
  • Added JAR resolution system with priority: user option, Maven cache, then bundled (legacy fallback)
  • Replaced all class() == checks with inherits() for proper S4 class handling
  • Fixed implicit S4 generic imports from BiocGenerics (colnames, rownames, ncol, nrow)
  • Improved package startup messages using cli formatting
  • Consolidated GitHub Actions workflows into a single ci.yaml
  • Added unit tests for setup, constants, and package loading
  • Added BiocGenerics to Imports; digest and withr to Suggests

rTASSEL 0.10.0

rTASSEL 0.9.33

rTASSEL 0.9.32

  • 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()

rTASSEL 0.9.31

  • 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.

rTASSEL 0.9.30

  • 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

rTASSEL 0.9.29

  • Added genotype table summary methods:
  • 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:
  • Added read method for importing GIGWA data through QBMS:

rTASSEL 0.9.28

  • 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

rTASSEL 0.9.27

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

rTASSEL 0.9.26

  • 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.

rTASSEL 0.9.25

  • Bug fixes:
    • Fixed character conversion bug in DataFrame object returns.
  • pca() can optionally report eigenvalues and eigenvectors as a list object.
  • Added new function:
  • Added new function:
    • imputLDKNNi()
    • Allows for LD KNNi imputation of GenotypeTable objects.

rTASSEL 0.9.24

  • 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.

rTASSEL 0.9.23

  • 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:
  • 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()

rTASSEL 0.9.22

  • Fix manhattanPlot() aesthetics:
    • Remove redundant marker labels from x-axis
    • Change x-axis label to SNP Positions

rTASSEL 0.9.21

rTASSEL 0.9.20

rTASSEL 0.9.19

  • 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.

rTASSEL 0.9.18

  • Added functions to calculate linkage disequilibrium (LD)
  • Proposed LD functions:

rTASSEL 0.9.17

  • Added new function:
    • manhattanPlot()
  • Removed tidyverse dependencies

rTASSEL 0.9.16

  • 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

rTASSEL 0.9.13

  • Added error checks for catching C stack usage errors for the following functions:
    • filterGenotypeTableSites()
    • filterGenotypeTableTaxa()
  • Added NEWS file for tracking version updates.

rTASSEL 0.9.12

  • Added new functions:
    • leaveOneFamilyOut()
    • genomicPredction()
  • Fixed a bug where tibbles when passed through readPhenotypeFromDataFrame(), would cause errors.