Changelog • rTASSEL

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()

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

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

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.

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.

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.

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()

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

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.

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.

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

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

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

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