************************************************** * * * 1.0系列新闻 * * * ************************************************** 阿GENOMINATOR 1.1版本新特性的变化包括一个例子在装饰图案与启动权重以及部分基因模型。o添加computePrimingWeights和addPrimingWeights;这是作者最近开发的一种方法，试图使RNA-Seq读取在表达的转录本中更加均匀分布。o makeGeneRepresentation已经添加并公开。该函数基于注释计算Union、Union- intersection、Background和Regions of constant expression (ROCEs)。o validAnnotation现在是公共的。o初始重写“使用ShortRead包”小短文，其中将包含对来自yeastRNASeq包的数据进行完全可行的分析。o新闻文件现在可以通过R函数调用NEWS (package = "Genominator")解析。更改importFromAlignedReads只有一个参数'x'，而不是'aligned dreads '和'filename '。o添加功能的importFromAlignedReads，使它可以立即崩溃几个文件在一起，以代价有他们在同一时间的所有内存(这一点稍后可能会改变)。 o Added groupBy to summarizeByAnnotation. o Added to Bioconductor. o Improved User Guide substantially o Added CITATION file. BUG FIXES o Fixed a bug related to the deprecation of IRanges::matchMatrix. o Fixed two bugs discovered by Elizabeth Purdom regarding wrong indexing in .writeRegionsTable and importToExpData. o Changed some internals of the plotting functionality to make it work with a GenomeGraphs update. o The new version of DBI (0.2-5) fixes the name mangling of the SQL reserved keyword "end". Workarounds for this mangling has been removed and Genominator now depends on DBI >= 0.2-5. o Added a check to importToExpData so that only rows with non-missing values of (chr, location, strand) gets written to the database. o Fixed the connection pool to be outside of individual ExpData objects. This elucidated a hitherto unknown bug where a user could inadvertently write to a read-only database. o (Internal) Changed a few tryCatch statements to use the SQL "... IF EXISTS ..." instead. o Changed the db and filename to be in sync: there is now only a dbFIlename slot in ExpData and all functions accept dbFilename. CHANGES IN GENOMINATOR VERSION 1.0 NEW FEATURES o Changed underlying database model where now the database exists in two modes, either a read or write mode. This should be somewhat transparent to the end user. o Added importFromAlignedRead which allows the importing of objects read using readAligned from ShortRead package. o Added support for arbitrary index columns, this support allows for the inclusion of more complex types of reads, e.g. reads of different lengths or paired end reads. This support is preliminary, but should allow for a mix of representations. o Added '$' and '[' methods to expData objects to directly query the database. o Fixed vignette to more correctly describe splitByAnnotation. o Added ability to filter the reads when importing an Eland export file. o Added whereClause to summarizeExpData. o Added sample = FALSE argument to plot function for goodness of fit plots. This allows one to plot fewer than all of the points for smaller pdfs. o Added regionGoodnessOfFit.df to work with matrices or data.frames. o Added in-memory ordering to importToExpData; this speeds things up considerably when indexing. BUG FIXES o Fixed bug where colnames are trashed when preserveColnames = T and bindAnno = T o Modified fix below when we include "what" argument. o Fixed bug in splitByAnnotation when expand = TRUE and addOverStrands = TRUE and only one strand was present in the sequencing reads. o Fixed bug in splitByAnnotation when expand = TRUE where reads were lost. %%%% Local Variables: %%%% mode: change-log %%%% coding: utf-8 %%%% End: