r2
parameter bug in ldPlot()
_
values now replace spaces.show()
method for TasselDistanceMatrix
objects.seqDiversity()
DataFrame
object returns.pca()
can optionally report eigenvalues and eigenvectors as a list object.imputeNumeric()
GenotypeTable
objects.imputLDKNNi()
GenotypeTable
objects.TasselDistanceMatrix
classkinshipMatrix()
and distanceMatrix()
) now return an object of type TasselDistanceMatrix
.colnames()
, rownames()
, ncol()
, and nrow()
will return relative information similar to how these operate with matrix
type objects.as.matrix()
now supersedes deprecated functions kinshipToRMatrix()
and distanceToRMatrix()
.readTasselDistanceMatrix()
asTasselDistanceMatrix()
matrix
to an object of type TasselDistanceMatrix
.createTree()
Neighbor_Joining
and UPGMA
methodstreeJavaApp()
createTree()
manhattanPlot()
aesthetics:SNP Positions
filterGenotypeTableSites()
gRangesObj
: Filter genotype tables by using a GRanges
object.filterGenotypeTableTaxa()
taxa
: Pass a vector of taxa IDs to filter genotype table by.getSumExpFromGenotypeTable()
bug:NA
s instead of 128
values.filterGenotypeTableSites()
removeMinorSNPStates
: Boolean; removes minor SNP states.removeSitesWithIndels
: Boolean; removes sites with indels.filterGenotypeTableSites()
siteRangeFilterType
parameter bug in filterGenotypeTableSites()
. Now defaults to none
when user does not specify filter type.getSumExpFromGenotypeTable()
coerceDosageToInt
: Returns raw byte dosage array instead of integer from Java.verbose
: Display console messages for large “memory-intensive” datasets.linkageDiseq()
- Returns TASSEL LD table report as data frameldPlot()
- Returns static ggplot2
plotldJavaApp()
- Initiates TASSEL’s interactive LD viewerleaveOneFamilyOut()
genomicPredction()
readPhenotypeFromDataFrame()
, would cause errors.