版本变化1.17.8:o添加方法alleleCount返回的等位基因数。改变版本1.17.7:o Bug修复在SeqVarData alleleFrequency方法频率计算做了两次,因为第一计算没有返回。的变化版本1.17.6:o选项添加到返回交替等位基因剂量使用矩阵的稀疏矩阵包。o提高阅读速度使用seqBlockApply剂量。版本变化1.17.2:o变化实现迭代器类的识别指标的选定的变体在variantList插槽对象创建和存储。现在所有的迭代器类扩展新的类SeqVarIterator。版本变化1.15.3:o alleleFrequency方法占性计算频率X和Y染色体。改变版本1.15.2:o添加迭代器类:SeqVarBlockIterator, SeqVarRangeIterator, SeqVarWindowIterator SeqVarListIterator。o创建SeqVarData对象与缺失的样本或变量注释将存储0-column sampleData或variantData数据帧,而不是复制样品。id和variant.id。o添加方法返回变体数据扩展形式,与每一行替代等位基因。 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