NEWS

---

betterChromVAR 1.1.12

New features

• smoothDeviationsKNN(): adaptive EB smoothing of single-cell deviations across nearest-neighbor cells.

Bug fixes

• Fixed wrong denominator in computeDeviationsWeighted
• Fixed mistake in background variance (affecting the scale of the z-scores): it is now the variance of the counts of each bin's background peaks (as would be drawn by sampleBackgroundPeaks()), and shrinkage is only applied to the expectation.

Changes

• The z-scores (and things based on it, e.g. motif variability) now include a finite-population correction (fpc=TRUE) of the null variance.
• functions now also return an effective N per motif that is used in normalizeDevsForSize for more accurate adjustment.

betterChromVAR 1.1.9

• Fixed bug that some SE-like objects were not recognized as such

betterChromVAR 1.0.8

• Added methods for kNN-based background

betterChromVAR 1.0.2

Bug fixes

• Fixed namespace error in getBackgroundBins when using dgCMatrix counts
• Fixed bug in the binning when using frag length bias
• Fixed delay in betterChromVAR

betterChromVAR 1.0.0

Initial release.