Changelog

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.