NEWS.md

rTASSEL 0.9.33

• 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

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:
  • 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()

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:
  • imputeNumeric()
  • Allows for numeric imputation of GenotypeTable objects.
• 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:
  • 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()

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

• Added new function:
  • exportGenotypeTable()
• Added new vignette:
  • "Filtering Genotype Tables"

rTASSEL 0.9.20

• Added new parameter to filterGenotypeTableSites()
  • gRangesObj: Filter genotype tables by using a GRanges object.
• Added new parameter to filterGenotypeTableTaxa()
  • taxa: Pass a vector of taxa IDs to filter genotype table by.
• Fixed getSumExpFromGenotypeTable() bug:
  • dosage array now returns NAs instead of 128 values.

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:
  • linkageDiseq() - Returns TASSEL LD table report as data frame
  • ldPlot() - Returns static ggplot2 plot
  • ldJavaApp() - Initiates TASSEL's interactive LD viewer

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.