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| $-method | readParam class and methods |
| asDGEList | SummarizedExperiment to DGEList |
| asDGEList-method | SummarizedExperiment to DGEList |
| calculateCPM | Calculate CPM |
| checkBimodality | Check bimodality of regions |
| cluster-direction | Reporting cluster-level direction in 'csaw' |
| clusterFDR | Compute the cluster-level FDR |
| clusterWindows | Cluster DB windows into clusters |
| clusterWindowsList | Consolidate DB clusters |
| combineOverlaps | Combine statistics for overlap-based clusters |
| combineTests | Combine statistics across multiple tests |
| consolidateOverlaps | Defunct functions |
| consolidateTests | Defunct functions |
| consolidateWindows | Defunct functions |
| controlClusterFDR | Compute the cluster-level FDR |
| correlateReads | Compute correlation coefficients between reads |
| csaw | View csaw user's guide |
| csawUsersGuide | View csaw user's guide |
| defunct | Defunct functions |
| detailRanges | Add annotation to ranges |
| empiricalFDR | Control the empirical FDR |
| empiricalOverlaps | Combine statistics for overlap-based clusters |
| extractReads | Extract reads from a BAM file |
| filterWindows | Defunct functions |
| filterWindowsControl | Filtering methods for RangedSummarizedExperiment objects |
| filterWindowsGlobal | Filtering methods for RangedSummarizedExperiment objects |
| filterWindowsLocal | Filtering methods for RangedSummarizedExperiment objects |
| filterWindowsProportion | Filtering methods for RangedSummarizedExperiment objects |
| findMaxima | Find local maxima |
| findOverlapsList | Consolidate window sizes |
| getBestOverlaps | Combine statistics for overlap-based clusters |
| getBestTest | Get the best test in a cluster |
| getPESizes | Compute fragment lengths for paired-end tags |
| getWidths | Get region widths |
| maximizeCcf | Find the delay at the maximal CCF |
| mergeResults | Wrappers to get region-level results |
| mergeResultsList | Wrappers to combine multiple analyses |
| mergeWindows | Merge windows into clusters |
| mergeWindowsList | Consolidate window sizes |
| minimalTests | Require rejection of a minimal number of tests |
| mixedClusters | Tests for mixed DB clusters |
| mixedOverlaps | Combine statistics for overlap-based clusters |
| mixedTests | Tests for mixed DB clusters |
| normFactors | Normalize counts across libraries |
| normOffsets | Normalize counts across libraries |
| overlapResults | Wrappers to get region-level results |
| overlapResultsList | Wrappers to combine multiple analyses |
| overlapStats | Combine statistics for overlap-based clusters |
| profileSites | Profile binding sites |
| readParam | readParam class and methods |
| readParam-class | readParam class and methods |
| reform | readParam class and methods |
| reform-method | readParam class and methods |
| regionCounts | Count reads overlapping each region |
| scaleControlFilter | Filtering methods for RangedSummarizedExperiment objects |
| scaledAverage | Scaled average abundance |
| show-method | readParam class and methods |
| strandedCounts | Get strand-specific counts |
| summitOverlaps | Combine statistics for overlap-based clusters |
| upweightSummit | Upweight summits |
| windowCounts | Count reads overlapping each window |
| wwhm | Window width at half maximum |