NEWS.md

In maize-genetics/rTASSEL: R Front-End for TASSEL

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.

maize-genetics/rTASSEL documentation built on Nov. 13, 2023, 7:18 a.m.