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