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rTASSEL 0.9.29
- Added genotype table summary methods:
-
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:
- Added read method for importing GIGWA data through
QBMS
:
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:
- 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:
- 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:
- Added new vignette:
- “Filtering Genotype Tables”
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:
rTASSEL 0.9.17
- Added new function:
- Removed tidyverse dependencies
rTASSEL 0.9.16
- Added write to file parameters for:
- Added p-value threshold parameters for:
- Added thread usage paramters for:
- 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.