Man pages for GabrielHoffman/decorate
Differential Epigenetic Coregulation Test

boxMBox's M-test
boxM_fastBox's M-test
boxM_permuteBox's M-test
collapseClustersCollapse clusters based on jaccard index
combineResultsCombine results into a single data.frame
corrMatrix.testTest difference between two correlation matricies
corSubsetPairsCompute correlations between pairs of features
countClusters-methodsCount clusters on each chromosome
createClustersCreate cluster from list of hclust objects
createCorrelationMatrixCreate correlation matrix
decorateDataSimulated data to show correlation clustering
delaneau.scoreScore impact of each sample on correlation sturucture
delaneau.testTest association between correlation sturucture and variable
dot-evalDiffCorrInternal .evalDiffCorr
epiclust-classClass epiclust
epiclustDiscreteList-classClass epiclustDiscreteList
epiclustDiscreteListContain-classClass epiclustDiscreteListContain
epiclustList-classClass epiclustList
evalDiffCorr-methodsEvaluate Differential Correlation
evaluateCorrDecayEvaluate the decay of correlation versus distance between...
extractCorrelationScoresExtract sample-level correlation scores
filterClustersExtract subset of clusters
getClusterNamesGet name of each cluster
getClusterRangesGet genome coordinates for each cluster
get_exon_coordsGet coordinates of exons
getFeaturesInClusterGet feature names in selected cluster
getFeaturesInClusterListGet feature names in selected cluster
getPeakDistancesCompute distance between peaks
getSubset-methodsExtract subset of data points
ggplot_by_samplingPlot by subsampling in each bin
jaccardEvaluate Jaccard index
makeImageRectConvert correlation matrix into triangle plot
plotClusterSegmentsPlot cluster segments
plotCompareCorrPlot two correlation matrices together
plotCorrDecayPlot correlation delay
plotCorrTrianglePlot triangle of correlation matrix
plotDecoratePlot decorate analysis
plotDensityPointsPlot density as color, add outlier points
plotEnsGenesPlot ENSEMBL genes
plotGenesPlot genes from a specified region of the human genome.
plotPairwiseScatterScatter plot of all pairs of variables stratified by test...
plotScatterPairsScatter plot of all pairs of variables stratified by test...
retainClustersRetain clusters by applying filter
runFastStatTest difference in correlation using closed form tests
runOrderedClusteringRun hierarchical clustering preserving order
runOrderedClusteringGenomeRun hierarchical clustering preserving order
runPermutedDataRun hierarchical clustering permuting features
scoreClustersCompute scores for each cluster
sLEDresults-classAn S4 class that stores results of sLED analysis
sle.scoreScore impact of each sample on sparse leading eigen-value
sle.testTest association between sparse leading eigen-value and...
sub-epiclustDiscreteListContain-ANY-ANY-ANY-methodAllow subsetting of epiclustDiscreteListContain
summary-sLEDresults-methodSummarize sLED analysis
whichClusterFind which cluster a peak is in
GabrielHoffman/decorate documentation built on July 26, 2021, 12:18 a.m.