NEWS

recoup 1.31.1 (2023-03-14)

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).
More supported genomes
Quick, high-level profile based on RPM instead of coverage
Speed and code improvements

Fixed bug resulting in running the same operation multiple times when chunking was requested.

New faster annotation building system which keeps also versions. May break older annotation stores. A rebuild is advised.
More supported genomes

Fixed a bug resulting in profile bleeding when using a mask of ranges from a BAM file.

Major improvements in speed and memory consumption.
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.
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
Chunking of large regions in now an option. Further reduces memory usage for large genomic regions with large BAM files.

Added support for BigWig files which greatly increases coverage reading speed.
Added plyr import to reduce memory footprints in some averaging calculations.
Added another plot type which shows correlation between average coverage in summarized genomic regions and respective plot control parameters.
Plotting of confidence intervals for profile (and the newly added correlation) plots (geom_ribbon) is now an option.
The setter function now supports mulitple argument setting at once.
Object slicing is now also performed on genomic position instead of only reference regions and samples.
Stopped automatic width in heatmaps and passed control to the user through the use of ... and also using ... for plots rendered with ggplot.
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.
Added documentation for recoup_test_data
Added small BAM files for testing of the preprocessRanges()) function.
Updated vignettes.

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'.
Fixed bug when region is "custom" and the intervals were not of fixed width. Credits to Orsalia Hazapis, BSRC 'Alexander Fleming'.
Fixed bug in custom heatmap ordering.
Fixed bug in calculation of average profiles in recoupCorrelation when using mean/median instead of splines.

Removed bigmemory/biganalytics as storage is a trouble.
Added (almost) full reusability of recoup objects. Now the most serious, memory and time consuming calculations need to perform just once.
Added slicing/subsetting or recoup list object.
Broke the code in more collated files.
k-means design function is now much more flexible.

Added a global sampling factor to reduce the size of the total reads and genomic areas for fast overviews.
Coverages and profiles are not recalculated when only ordering (k-means or other) changes.
Exported kmeansDesign and removeData functions.
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.
Reduced binned coverage calculation time by two
Switched to bigmemory and biganalytics packages to handle coverage profile matrices.
Added sample subsetting when plotting. In this way, profiles are computed once and the user may choose what to plot later.
Added a simple setter and getter for easier manipulation and reusability of recoup objects.