# 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

