版本0.1.0的变化(2016-01-18)-------------------------------------新功能o首次发布版本0.2.0的变化(2016-01-28)-------------------------------------新功能o增加了一个全局采样因子，以减少总reads和基因组区域的大小，以便快速概述。o仅在排序(k-means或其他)更改时，不重新计算覆盖范围和配置文件。o导出kmeansDesign和removeData函数。o增加了补偿输出列表对象的完全可重用性。在使用此对象的调用中，仅根据输入参数的变化重新计算所需的元素，为简单的绘图/剖面排序/分箱更改节省了大量计算时间。o切换到bigmemory和biganalytics包来处理覆盖配置文件矩阵。o绘图时增加了样本子集。通过这种方式，轮廓只计算一次，用户可以选择以后绘制什么。o增加了一个简单的setter和getter，更容易操作和可重用的补偿对象。BUG修复o修复了标题和曲线尺寸的问题在一些图表0.4.0版本的变化(2016-02-02)-------------------------------------新功能o删除大内存/大分析作为存储是一个麻烦。 o Added (almost) full reusability of recoup objects. Now the most serious, memory and time consuming calculations need to perform just once. o Added slicing/subsetting or recoup list object. o Broke the code in more collated files. o k-means design function is now much more flexible. BUG FIXES o Fixed bug with colors in curve profile single-design plots. CHANGES IN VERSION 0.99.4 (2016-04-02) ------------------------------------- NEW FEATURES o Added support for BigWig files which greatly increases coverage reading speed. o Added plyr import to reduce memory footprints in some averaging calculations. o Added another plot type which shows correlation between average coverage in summarized genomic regions and respective plot control parameters. o Plotting of confidence intervals for profile (and the newly added correlation) plots (geom_ribbon) is now an option. o The setter function now supports mulitple argument setting at once. o Object slicing is now also performed on genomic position instead of only reference regions and samples. o Stopped automatic width in heatmaps and passed control to the user through the use of ... and also using ... for plots rendered with ggplot. o Moved sumStat and smooth options from binParams to plotParams as smoothing should be available for reusing/replotting recoup objects. sumStat remained in binParams to be used for region binning over e.g. gene bodies. o Added documentation for recoup_test_data o Added small BAM files for testing of the preprocessRanges()) function. o Updated vignettes. BUG FIXES o Fixed bug when reading reads from bed files. GenomeInfoDb is used to fill the seqinfo slot of the produced GenomicRanges. Credits to Orsalia Hazapis, BSRC 'Alexander Fleming'. o Fixed bug when region is "custom" and the intervals were not of fixed width. Credits to Orsalia Hazapis, BSRC 'Alexander Fleming'. o Fixed bug in custom heatmap ordering. o Fixed bug in calculation of average profiles in recoupCorrelation when using mean/median instead of splines. CHANGES IN VERSION 1.1.3 (2017-04-03) ------------------------------------- NEW FEATURES o Major improvements in speed and memory consumption. o RNA-Seq plots can now use pre-calculated ranges. This is advised for these plots as on-the-fly GenomicRanges manipulations can take time. See details in the buildAnnotationStore function. o Added a function for merging runs. This is very useful in the case of having to analyze many files including large regions (e.g. gene bodies o Chunking of large regions in now an option. Further reduces memory usage for large genomic regions with large BAM files. BUG FIXES o Fixed some bugs when using external annotations and on-the-fly calculations. CHANGES IN VERSION 1.7.2 (2018-04-25) ------------------------------------- NEW FEATURES o New faster annotation building system which keeps also versions. May break older annotation stores. A rebuild is advised. o More supported genomes BUG FIXES o Fixed a bug resulting in profile bleeding when using a mask of ranges from a BAM file. CHANGES IN VERSION 1.17.1 (2020-05-03) ------------------------------------- NEW FEATURES o New annotation based on an SQLite database. Rebuild must be performed otherwise the application will break. Download of a ready made annotation is also available (see vignette). o More supported genomes o Quick, high-level profile based on RPM instead of coverage o Speed and code improvements BUG FIXES o Fixed bug resulting in running the same operation multiple times when chunking was requested.