NEWS.md

In GabrielHoffman/decorate: Differential Epigenetic Coregulation Test

decorate 1.0.31

May 17, 2023

• fix bug https://github.com/GabrielHoffman/decorate/issues/2

decorate 1.0.30

Sept 13, 2022

- Update dependencies

decorate 1.0.29

July 23, 2021

- small updates to documentation with `pkgdown`

decorate 1.0.28

July 8, 2021

- incorporate new faster version of adjclust package (>= 0.6.0)

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 group

decorate 1.0.25

September 6, 2019

- use density plot for plotCorrDecay()

decorate 1.0.24

August 22, 2019

- add options for plotCorrDecay()

decorate 1.0.23

August 5, 2019

- fix bug in evaluateCorrDecay() when chromosome has no peaks

decorate 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 covariance

decorate 1.0.21

August 2, 2019

- fix bug in evalDiffCorr() preventing running "deltaSLE" with multiple categories

decorate 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 1.0.19

July 26, 2019

- getClusterRanges() and combineResults() is much faster

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 1.0.16

June 5, 2019

- improve error message in plotDecorate()

decorate 1.0.15

May 29, 2019

- improve error messages for retainClusters()
- add combineResults()
- add additional plots to vignette

decorate 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 page

decorate 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 genes

decorate 1.0.9

March 22, 2019

- enable analysys of clusters of size 3

decorate 1.0.9

March 17, 2019

- export classes so objects restore correctly from load()

decorate 1.0.8

March 7, 2019

- fix error in evaluateCorrDecay()

decorate 1.0.7

March 4, 2019

- GRanges object uses names(gr) feature 
- drop chromosomes from GRanges objects if they don't have any entries

decorate 1.0.6

Feb 28, 2019

- fix plotDecorate() for intervals with no genes
- fix collapseClusters() and plotDecorate() error with feature names

decorate 1.0.5

Feb 27, 2019

- plotDecorate() now plots genes
- much faster collapseClusters()

decorate 1.0.4

Feb 25, 2019

- Fix small bugs in syntax
- update vignette to new workflow
- update readme

decorate 1.0.3

Feb 22, 2019

- add retainClusters() to process results of scoreClusters()
- chance synatax of filterClusters()
- add collapseCluster() to drop redundant clusters
- countClusters() fix

decorate 1.0.2

Feb 21, 2019

- Add genes to plotDecorate()
- add handling of multiple clustering cutoff parameters
- parallelize scoreClusters()

decorate 1.0.1

- add evaluateCorrDecay()
- fix plotting for plotDecorate() and plotCompareCorr()

decorate 1.0.0

- Release

decorate 0.99.3

- fix issues with ploting trees

decorate 0.99.2

- reduce memory usage substantially
- reduce compute time 100x by using adaptive permutations

decorate 0.99.1

Jan 22, 2019

- Initial version

GabrielHoffman/decorate documentation built on May 23, 2023, 1:29 a.m.