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Recent Releases of rTASSEL

rTASSEL - v0.10.0

  • Updated JARs to TASSEL 5.2.96
  • Updated formula parsing:
    • Drop and keep traits by using - and +, respectively
    • Added keywords to drop/keep all covariate or factor traits:
    • I(cov)
    • I(fct)
  • Added stepwiseModelFitter() function:
  • Added new function readNumericGenotypeFromRMatrix() (https://github.com/maize-genetics/rTASSEL/issues/15):
    • Converts formatted R matrix to TASSEL 5 numeric genotype
  • Added experimental function readGenotype():
    • Reads data into new TasselGenotype class (future update)
    • Dynamically read genotype data based on data type
  • Added experimental function readPhenotype():
    • Reads data into new TasselPhenotype class (future update)
    • Dynamically read phenotype data based on data type
  • Added deprecation warnings to the following methods:
    • getPhenotypeDF()
    • getSumExpFromGenotypeTable()
    • readGenotypeTableFromPath()
    • readGenotypeTableFromGigwa()
    • readGenotypePhenotype()
    • readPhenotypeFromDataFrame()
    • readPhenotypeFromPath()
    • ldJavaApp()
    • treeJavaApp()
    • NOTE: these will be removed in future updates
  • Updated vignettes:
    • Visualization section updates
    • Formula parsing
    • AssociationResults and PCAResults object handling
    • Memory allocation guide (https://github.com/maize-genetics/rTASSEL/issues/16)
    • Numeric genotype handling
  • Updated website CSS

Scientific Software - Peer-reviewed - R
Published by btmonier 10 months ago

rTASSEL - 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

Scientific Software - Peer-reviewed - R
Published by btmonier over 2 years ago

rTASSEL - 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

Scientific Software - Peer-reviewed - R
Published by btmonier over 2 years ago

rTASSEL - 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()

Scientific Software - Peer-reviewed - R
Published by btmonier over 3 years ago

rTASSEL - 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

Scientific Software - Peer-reviewed - R
Published by btmonier over 3 years ago

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.

Scientific Software - Peer-reviewed - R
Published by btmonier over 3 years ago

rTASSEL - 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.

Scientific Software - Peer-reviewed - R
Published by btmonier over 3 years ago

rTASSEL -

  • 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()

Scientific Software - Peer-reviewed - R
Published by btmonier over 4 years ago