Man pages for GabrielHoffman/decorate
Differential Epigenetic Coregulation Test
| boxM | Box's M-test |
| boxM_fast | Box's M-test |
| boxM_permute | Box's M-test |
| collapseClusters | Collapse clusters based on jaccard index |
| combineResults | Combine results into a single data.frame |
| corrMatrix.test | Test difference between two correlation matricies |
| corSubsetPairs | Compute correlations between pairs of features |
| countClusters-methods | Count clusters on each chromosome |
| createClusters | Create cluster from list of hclust objects |
| createCorrelationMatrix | Create correlation matrix |
| decorateData | Simulated data to show correlation clustering |
| delaneau.score | Score impact of each sample on correlation sturucture |
| delaneau.test | Test association between correlation sturucture and variable |
| dot-evalDiffCorr | Internal .evalDiffCorr |
| epiclust-class | Class epiclust |
| epiclustDiscreteList-class | Class epiclustDiscreteList |
| epiclustDiscreteListContain-class | Class epiclustDiscreteListContain |
| epiclustList-class | Class epiclustList |
| evalDiffCorr-methods | Evaluate Differential Correlation |
| evaluateCorrDecay | Evaluate the decay of correlation versus distance between... |
| extractCorrelationScores | Extract sample-level correlation scores |
| filterClusters | Extract subset of clusters |
| getClusterNames | Get name of each cluster |
| getClusterRanges | Get genome coordinates for each cluster |
| get_exon_coords | Get coordinates of exons |
| getFeaturesInCluster | Get feature names in selected cluster |
| getFeaturesInClusterList | Get feature names in selected cluster |
| getPeakDistances | Compute distance between peaks |
| getSubset-methods | Extract subset of data points |
| ggplot_by_sampling | Plot by subsampling in each bin |
| jaccard | Evaluate Jaccard index |
| makeImageRect | Convert correlation matrix into triangle plot |
| plotClusterSegments | Plot cluster segments |
| plotCompareCorr | Plot two correlation matrices together |
| plotCorrDecay | Plot correlation delay |
| plotCorrTriangle | Plot triangle of correlation matrix |
| plotDecorate | Plot decorate analysis |
| plotDensityPoints | Plot density as color, add outlier points |
| plotEnsGenes | Plot ENSEMBL genes |
| plotGenes | Plot genes from a specified region of the human genome. |
| plotPairwiseScatter | Scatter plot of all pairs of variables stratified by test... |
| plotScatterPairs | Scatter plot of all pairs of variables stratified by test... |
| retainClusters | Retain clusters by applying filter |
| runFastStat | Test difference in correlation using closed form tests |
| runOrderedClustering | Run hierarchical clustering preserving order |
| runOrderedClusteringGenome | Run hierarchical clustering preserving order |
| runPermutedData | Run hierarchical clustering permuting features |
| scoreClusters | Compute scores for each cluster |
| sLEDresults-class | An S4 class that stores results of sLED analysis |
| sle.score | Score impact of each sample on sparse leading eigen-value |
| sle.test | Test association between sparse leading eigen-value and... |
| sub-epiclustDiscreteListContain-ANY-ANY-ANY-method | Allow subsetting of epiclustDiscreteListContain |
| summary-sLEDresults-method | Summarize sLED analysis |
| whichCluster | Find which cluster a peak is in |
