1.14版本的变化- - - - - - - - - - - - - - - - - - - - - - - - o键方法现在有新的参数新特性允许更复杂的过滤。o增加基因()器o makeTranscriptDbFromGFF()现在处理更多不同类型的人造石铺地面文件。BUG修复o更好的参数检查makeTranscriptDbFromGFF () o关口参数和方法将列参数和方法1.12版本的变化- - - - - - - - - - - - - - - - - - - - - - - -新特性支持新的UCSC的物种o更好地支持GTF和人造石铺地面处理成TranscriptDb对象o方法让TranscriptDb对象一般来源进行了更有用的BUG修复o更新允许继续使用不断变化的服务,比如UCSC的o / o修正seqnameStyle方法处理GTF 10倍的性能收益和人造石铺地面文件1.10版本的变化- - - - - - - - - - - - - - - - - - - - - - - -阿新特性添加makeTranscriptDbFromGFF ()。用户现在可以使用人造石铺地面文件TranscriptDb资源。o添加* *”限制seqinfo <——“TranscriptDb对象的方法。它只支持替换序列的名称(现在),即序列,除了他们的名字,Seqinfo对象“价值”(提供)和“Seqinfo (x)”(当前)必须是相同的。o添加促进剂()和getPromoterSeq ()。阿加的重新分配。默认id参数(假)makeTranscriptDb ()。 SIGNIFICANT USER-VISIBLE CHANGES o Updated vignette. o Improve how makeTranscriptDbFromUCSC() and makeTranscriptDbFromBiomart() assign internal ids (see commit 65144 for the details). o 2.5x speedup of fiveUTRsByTranscript() and threeUTRsByTranscript(). DEPRECATED AND DEFUNCT o Are now defunct: transcripts_deprecated(), exons_deprecated(), and introns_deprecated(). o Deprecate loadFeatures() and saveFeatures() in favor of loadDb() and saveDb(), respectively. BUG FIXES o Better handling of BioMart data anomalies. CHANGES IN VERSION 1.8 ----------------------- NEW FEATURES o Added asBED and asGFF methods to convert a TranscriptDb to a GRanges that describes transcript structures according to either the BED or GFF format. This enables passing a TranscriptDb object to rtracklayer::export directly, when targeting GFF/BED. CHANGES IN VERSION 1.6 ----------------------- NEW FEATURES o TranscriptDbs are now available as standard packages. Functions that were made available before the last release allow users to create these packages. o TranscriptDb objects now can be used with select o select method for TranscriptDb objects to extract data.frames of available annotations. Users can specify keys, along with the keytype, and the columns of data that they want extracted from the annotation package. o keys now will operate on TranscriptDB objects to expose ID types as potential keys o keytypes will show which kinds of IDs can be used as a key by select o cols will display the kinds of data that can be extracted by select o isActiveSeq has been added to allow entire chromosomes to be toggled active/inactive by the user. By default, everything is exposed, but if you wish you can now easily hide everything that you don't want to see. Subsequence to this, all your accessors will behave as if only the "active" things are present in the database. SIGNIFICANT USER-VISIBLE CHANGES o saveDb and loadDb are here and will be replacing saveFeatures and loadFeatures. The reason for the name change is that they dispatch on (and should work with a wider range of object types than just trancriptDb objects (and their associated databases). BUG FIXES o ORDER BY clause has been added to SQL statements to enforce more consistent ordering of returned rows. o bug fixes to enable DB construction to still work even after changes in schemas etc at UCSC, and ensembl sources. o bug fixes to makeFeatureDbFromUCSC allow it to work more reliably (it was being a little too optimistic about what UCSC would actually supply data for)