Changes in version 1.27.1
o Add 'parallel' argument to methods.
Changes in version 1.25.1
o Bug fix in minorAlleleCount when all samples have the same sex.
Changes in version 1.23.1
o Add minorAlleleCount method.
Changes in version 1.21.5
o getGenotype and getGenotypeAlleles work for haploid genotypes.
Changes in version 1.21.4
o Add vignette describing iterators.
Changes in version 1.21.1
o Add method to return imputed dosage.
Changes in version 1.19.4
o Reduce memory usage when creating a SeqVarData object.
Changes in version 1.19.3
o Rewrite the duplicateDiscordance method for a single GDS file
to be much faster and return output consistent with the
cross-file method.
Changes in version 1.19.2
o Add methods currentVariants and currentRanges for
SeqVarIterator classes.
Changes in version 1.17.8
o Add method alleleCount to return count of alleles.
Changes in version 1.17.7
o Bug fix in alleleFrequency method for SeqVarData where
frequency calculation was done twice because the first
calculation was not returned.
Changes in version 1.17.6
o Add option to return alternate allele dosage in a sparse matrix
using the Matrix package.
o Improve speed of reading dosages by using seqBlockApply.
Changes in version 1.17.2
o Change implementation of iterator classes to identify indices
of selected variants on object creation and store in
variantList slot. All iterator classes now extend new class
SeqVarIterator.
Changes in version 1.15.3
o alleleFrequency method accounts for sex when computing
frequency for X and Y chromosomes.
Changes in version 1.15.2
o Added iterator classes: SeqVarBlockIterator,
SeqVarRangeIterator, SeqVarWindowIterator, SeqVarListIterator.
o Creating a SeqVarData object with missing sample or variant
annotation will store 0-column data frames in sampleData or
variantData, instead of duplicating sample.id and variant.id.
o Added methods to return variant data in expanded form, with one
row per alternate allele.
Changes in version 1.15.1
o Following SeqArray, remove dependency on VariantAnnotation
o Add generic isSNV (replacing previous import of this generic
from VariantAnnotation)
Changes in version 1.11.3
o Add hethom method to calculate heterozygosity / non-reference
homozygosity in one step
o Add countSingletons method
Changes in version 1.11.1
o Add variantData slot to SeqVarData class
Changes in version 1.9.11
o Add Firth test option to regression
o Bug fix for refFracPlot: hets significantly different from 0.5
plotted as triangles, median line shown
Changes in version 1.9.10
o duplicateDiscordance across two GDS files can calculate
discordance based on heterozygote/homozygote status instead of
genotype
Changes in version 1.9.9
o duplicateDiscordance across two GDS files can match on either
position or position and alleles, with the ability to recode
genotypes if th reference allele in one dataset is the
alternate allele in the other dataset
Changes in version 1.9.8
o duplicateDiscordance and alternateAlleleDetection require
SeqVarData objects; both can match on a subject.id instead of
sample.id
Changes in version 1.9.4
o alleleDosage returns list with dosage of each allele separately
Changes in version 1.9.2
o added by.variant option to duplicateDiscordance for two gds
files
Changes in version 1.7.9
o added more options to return dosage of different alleles
Changes in version 1.7.7
o added methods to calculate and plot reference allele fraction
Changes in version 1.7.6
o HWE method returns additional columns and allows permutation of
genotypes
Changes in version 1.7.5
o Added SeqVarData class to combine sample annotation with GDS
object
Changes in version 1.7.4
o HWE works on biallelic INDELs as well as SNVs
Changes in version 1.7.3
o Add methods for duplicateDiscordance with two datasets
o Add alternateAlleleDetection
Changes in version 1.5.1
o Use existing isSNV generic from VariantAnnotation instead of
redefining
o Use BiocStyle for vignette