decorate 1.0.27
November 25, 2019
- runOrderedClusteringGenome() requires rownames(X) to be found in names(gr)
- replace cat() with message()decorate 1.0.26
September 9, 2019
- in boxM_permute() return NA's if more variables than samples in the smallest groupdecorate 1.0.22
August 2, 2019
- in evalDiffCorr() return effect size estimates
- in sle.test() and delaneau.test()
if variable is factor with multiple levels, use Kruskal-Wallis test
if variable is factor with 2 levels, use Wilcoxon test
if variable is continuous, cor.test with spearman
- methods "Cai.max", "Chang.maxBoot", "LC.U", "WL.randProj", "Schott.Frob" now test correlation instead of covariancedecorate 1.0.21
August 2, 2019
- fix bug in evalDiffCorr() preventing running "deltaSLE" with multiple categoriesdecorate 1.0.20
July 31, 2019
- modify sle.score() to use lead eigen value of difference matrix
- add runPermutedData() to get cluster statistics from permuted data
- faster scoreClusters()
- plotCorrDecay() decorate 1.0.18
July 23, 2019
- add support for the following tests:
"Cai.max", "Chang.maxBoot", "LC.U.test", "WL.randProj", "Schott.Frob", "Delaneau", "deltaSLE"
- add extractCorrelationScores()
- add getClusterRanges()decorate 1.0.17
July 11, 2019
- reduce memory usage of evaluateCorrDecay()
- evalDiffCorr() now works on data.frame
- add corrMatrix.test()
- add support for following tests: "Box", "Box.permute", "Steiger.fisher", "Steiger", "Jennrich", "Factor", "Mann.Whitney", "Kruskal.Wallis"decorate 1.0.15
May 29, 2019
- improve error messages for retainClusters()
- add combineResults()
- add additional plots to vignettedecorate 1.0.14
May 28, 2019
- add plotScatterPairs()
- plotDecorate() can compute correlation matrix directly from data
- fixed bug in sign of sLED test statistic
- plotDecorate() and plotCompareCorr() now have argument absCorr=FALSE as default
- New simulated data
- add method "medianCorr" to evalDiffCorr()decorate 1.0.13
May 27, 2019
- apply droplevels() to testVariable in .evalDiffCorr() and plotCompareCorr()decorate 1.0.12
March 26, 2019
- whichCluster() accepts array for feature_id
- plotDecorate() and plotEnsGenes() now don't print empty pagedecorate 1.0.11
March 25, 2019
- whichCluster() results now have proper row names
- add function getFeaturesInClusterList()
- for plotDecorate(), expand allowable window to 5e7 bp for plotting genesdecorate 1.0.7
March 4, 2019
- GRanges object uses names(gr) feature
- drop chromosomes from GRanges objects if they don't have any entriesdecorate 1.0.6
Feb 28, 2019
- fix plotDecorate() for intervals with no genes
- fix collapseClusters() and plotDecorate() error with feature namesdecorate 1.0.4
Feb 25, 2019
- Fix small bugs in syntax
- update vignette to new workflow
- update readmedecorate 1.0.3
Feb 22, 2019
- add retainClusters() to process results of scoreClusters()
- chance synatax of filterClusters()
- add collapseCluster() to drop redundant clusters
- countClusters() fixdecorate 1.0.2
Feb 21, 2019
- Add genes to plotDecorate()
- add handling of multiple clustering cutoff parameters
- parallelize scoreClusters()