版本变化1.10.0 - - - - - - - - - - - - - - - - - - - - - - - -用户可见的变化o添加支持最新版本3.0 gnomAD加数据,存储在包MafDb.gnomAD.r3.0.GRCh38。o个体等位基因频率可以从MafDb检索。*包当“裁判”和“alt”参数的函数的gscores()”和“分数()”。看到手册页和装饰图案为进一步的细节。o NonSNRs现在搜索给findOverlaps参数类型=“平等”()。这意味着只有分数nonSNRs返回精确匹配。BUG修复BUG修复“getGScores阿()函数无法访问文件下载访问AnnotationHub o错误修复的加值从nonSNVs multiallelic变异从VCF文件存储在不同的记录。版本1.8.0的变化- - - - - - - - - - - - - - - - - - - - - - - -用户可见的变化o添加支持最新版本2.1升至GRCh38 gnomAD乘加数据的运用,MafDb.gnomAD.r2.1存储在包。GRCh38 MafDb.gnomADex.r2.1.GRCh38。BUG修复o错误修复在支持TOPMED乘加数据,抛弃变异的VCF过滤器没有设置为通过。1.6.0版本的变化- - - - - - - - - - - - - - - - - - - - - - - -用户可见的变化函数和类阿弃用先前版本(分数,MafDb类)现在已经从包中删除。 o Added support to latest release 2.1 of gnomAD MAF data, stored in packages MafDb.gnomAD.r2.1.hs37d5 and MafDb.gnomADex.r2.1.hs37d5. CHANGES IN VERSION 1.4.0 ------------------------ USER VISIBLE CHANGES o The function 'scores()' has been deprecated and replaced by the function 'gscores()'. o The argument 'scores.only' in the function 'scores()' has been deprecated and replaced by calling the function 'score()'. o The 'MafDb' class has been deprecated and now the 'GScores' class supports former 'MafDb' objects. The 'mafByOverlaps()' and 'mafById()' functions have been deprecated and replaced by the function 'gscores()'. The 'populations()' function from the 'MafDb' API has been integrated into the 'GScores' API. o Added metadata on genomic scores groups, available through the function 'gscoresGroups()', on availability of non-single nucleotide regions through the function 'gscoresNonSNRs()', and on the default population used through the function 'defaultPopulation()'. o New AnnotationHub resources have been added during this release cycle: phyloP60way.UCSC.mm10, LINSIGHT, phastCons46wayPlacental, phastcons46wayPrimates. o Added a BiocSticker at https://github.com/Bioconductor/BiocStickers/tree/master/GenomicScores o Added citation information after package publication has been accepted at Bioinformatics. CHANGES IN VERSION 1.2.0 ------------------------ USER VISIBLE CHANGES o Added methods 'name()' and 'type()' for GScores objects. o Enabled the retrieval of multiple score values per genomic position (e.g., as in CADD or M-CAP scores). o Added method 'citation()' to fetch citation information for genomic scores. o Added function 'makeGScoresPackage()' to create an annotation package from an AnnotationHub genomic scores resource. o Added 'qfun()' and 'dqfun()' methods to fetch the quantization and dequantization functions from used to store and retrieved genomic scores. o Added 'quantized' argument to the 'scores()' method to obtain quantized values if the user wants to dequantize the values him or herself. o Fallback to local AnnotationHub when there is no internet connection to fetch genomic scores through AnnotationHub resources. o Added 'MafDb' class, derived from 'GScores' to store and access minor allele frequency values. This was originally defined in the 'VariantFiltering' package. o The vignette has been updated to illustrate the use of some of the previous changes. CHANGES IN VERSION 0.99.0 ------------------------- USER VISIBLE CHANGES o Submission of the first version to the Bioconductor project. (start date: March 17, 2017)