# Change log Notable changes to this project will be documented in this file. ## [2.0.0] -- 2019-10-30 - Supervised analysis functionality added - Permutation testing for statistical significance - Major changes to user interface: parameter/function/output column name changes - runCOCOA => aggregateSignalGRList - loadingMat => signal - PCsToAnnotate => signalCol - orderByPC => orderByCol - regionGR => regionSet (some functions already had regionSet param) - pcScores => sampleScores - signalAlongPC => signalAlongAxis - cytosine_coverage (column name in output of runCOCOA()) => signalCoverage - region_coverage (column name in output of runCOCOA())=> regionSetCoverage - aggregateLoadings => aggregateSignal - getLoadingProfile => getMetaRegionProfile - total_region_number => totalRegionNumber - mean_region_size => meanRegionSize - regionQuantileByPC => regionQuantileByTargetVar - new column added to output of runCOCOA (only for multi-base data): sumProportionOverlap - for getMetaRegionProfile, scoringMetric => aggrMethod - for signalAlongAxis, pcScores => sampleScores - Addition of functionality for region-based data such as ATAC-seq - default setting automatically detects whether data is single base(e.g. DNA methylation or multiple bases like ATAC-seq. - different scoring method for single base vs multiple base data - Improved memory use/efficiency - Changed package data - Removed brcaLoadings1 object - Added DNA methylation data for more samples - Added ATAC-seq counts and associated coordinates - Added patient metadata for BRCA patients - Major changes to vignettes - reorganized vignettes into one long vignette - added ATAC-seq section - added supervised COCOA section - modified unsupervised DNA methylation section - Other changes - absVal parameter added for several functions (aggregateLoadings, getLoadingProfile, runCOCOA) - getMetaRegionProfile: default binNum changed from 25 to 21 - new function: getTopRegions() - add fitdistrplus and simpleCache dependencies - wilcoxon rank sum scoring method deprecated ## [1.0.2] -- 2019-03-06 - Bug fix: getLoadingProfile() had error when no overlap between signalCoord and regionSet. Now returns NULL in that case. - Bug fix: rsRankingIndex() was sorting NA's to the top of results. This is confusing when selecting top region sets for further analysis or visualization. Now NA's are sorted to the bottom. - Bug fix: rsScoreHeatmap() also was sorting NA's to the top of results, which resulted in potentially excluding the real top region sets from the plot. Now NA's are sorted to the bottom. ## [0.99.9] -- 2018-10-29 - First release version - Name changed to COCOA from PCRSA (Principal Component Region Set Analysis) - Other changes to UI including function names and parameters ## [0.99.0] -- 2018-09-05 - Submitted to Bioconductor