Man pages for LTLA/csaw
ChIP-Seq Analysis with Windows
| 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 |
| combineTests | Combine statistics across multiple tests |
| correlateReads | Compute correlation coefficients between reads |
| csawUsersGuide | View csaw user's guide |
| defunct | Defunct functions |
| detailRanges | Add annotation to ranges |
| empiricalFDR | Control the empirical FDR |
| extractReads | Extract reads from a BAM file |
| filterWindows | Filtering methods for RangedSummarizedExperiment objects |
| findMaxima | Find local maxima |
| 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 |
| mixedTests | Tests for mixed DB clusters |
| normFactors | Scaling normalization across libraries |
| normOffsets | Normalize trended biases across libraries |
| overlapStats | Combine statistics for overlap-based clusters |
| profileSites | Profile binding sites |
| readParam | readParam class and methods |
| regionCounts | Count reads overlapping each region |
| scaledAverage | Scaled average abundance |
| SEmethods | SummarizedExperiment to DGEList |
| strandedCounts | Get strand-specific counts |
| upweightSummit | Upweight summits |
| windowCounts | Count reads overlapping each window |
| wwhm | Window width at half maximum |
