$-method | readParam class and methods |
asDGEList | Statistical wrappers for RangedSummarizedExperiment objects |
asDGEList-method | Statistical wrappers for RangedSummarizedExperiment objects |
checkBimodality | Check bimodality of regions |
checkList | Get or modify readParam lists |
clusterFDR | Compute the cluster-level FDR |
combineOverlaps | Compute overlap statistics |
combineTests | Combine statistics across multiple tests |
consolidateSizes | Consolidate window sizes |
correlateReads | Compute correlation coefficients between reads |
csaw | View csaw user's guide |
csawUsersGuide | View csaw user's guide |
detailRanges | Add annotation to ranges |
dumpPE | Dump paired-end data to file |
extractReads | Extract reads from a BAM file |
filterWindows | Filtering methods for RangedSummarizedExperiment objects |
findMaxima | Find local maxima |
getBestOverlaps | Compute overlap statistics |
getBestTest | Get the best test in a cluster |
getPESizes | Compute fragment lengths for paired-end tags |
getWidths | Get region widths |
makeExtVector | Make an extVector object |
maximizeCcf | Find the delay at the maximal CCF |
mergeWindows | Merge windows into clusters |
normalize | Statistical wrappers for RangedSummarizedExperiment objects |
normalize-method | Statistical wrappers for RangedSummarizedExperiment objects |
normOffsets | Normalize counts between libraries |
normOffsets-method | Statistical wrappers for RangedSummarizedExperiment objects |
normOffsets-method | Normalize counts between libraries |
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 |
reformList | Get or modify readParam lists |
regionCounts | Count reads overlapping each region |
scaledAverage | Scaled average abundance |
show-method | readParam class and methods |
strandedCounts | Get strand-specific counts |
summitOverlaps | Compute overlap statistics |
upweightSummit | Upweight summits |
windowCounts | Count reads overlapping each window |
wwhm | Window width at half maximum |
[.extVector | Make an extVector object |