CHANGES IN VERSION 0.1.0 (2016-01-18) ------------------------------------- NEW FEATURES o First release CHANGES IN VERSION 0.2.0 (2016-01-28) ------------------------------------- NEW FEATURES o Added a global sampling factor to reduce the size of the total reads and genomic areas for fast overviews. o Coverages and profiles are not recalculated when only ordering (k-means or other) changes. o Exported kmeansDesign and removeData functions. o Added full reusability of the output list object of recoup. Upon a call using this object, only the required elements are recalculated according to the change in input parameters, saving a lot of computation time for simple plotting/profile ordering/binning changes. o Reduced binned coverage calculation time by two o Switched to bigmemory and biganalytics packages to handle coverage profile matrices. o Added sample subsetting when plotting. In this way, profiles are computed once and the user may choose what to plot later. o Added a simple setter and getter for easier manipulation and reusability of recoup objects. BUG FIXES o Fixed problem with title and curve sizes in some plots CHANGES IN VERSION 0.4.0 (2016-02-02) ------------------------------------- NEW FEATURES o Removed bigmemory/biganalytics as storage is a trouble. 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.