API for DMRcaller
Differentially Methylated Regions caller
| Global functions | |
|---|---|
| .analyseReadsInsideBins | Source code |
| .analyseReadsInsideBinsOneSample | Source code |
| .analyseReadsInsideBinsReplicates | Source code |
| .analyseReadsInsideRegions | Source code |
| .analyseReadsInsideRegionsForCondition | Source code |
| .analyseReadsInsideRegionsOneSample | Source code |
| .analyseReadsInsideRegionsReplicates | Source code |
| .computeAdjuestedPValues | Source code |
| .computeAdjuestedPValuesReplicates | Source code |
| .computeBetaReg | Source code |
| .computeBetaRegSingle | Source code |
| .computeDMRsBins | Source code |
| .computeDMRsNeighbourhood | Source code |
| .computeDMRsNoiseFilter | Source code |
| .computeDMRsReplicatesBins | Source code |
| .computeDMRsReplicatesNeighbourhood | Source code |
| .computeMethylationDataSpatialCorrelation | Source code |
| .computeProportionsInDMRs | Source code |
| .computeaAjustedPValuesInDMRs | Source code |
| .computeaAjustedPValuesInDMRsReplicates | Source code |
| .convertProportions | Source code |
| .convertResult | Source code |
| .countCytosinesInside | Source code |
| .countMethylationDataCoverage | Source code |
| .countOverlaps | Source code |
| .countTotalNumberOfCytosines | Source code |
| .epanechnicovKernel | Source code |
| .fisherTest | Source code |
| .fisherTestPValue | Source code |
| .gaussianKernel | Source code |
| .getLongestDMRs | Source code |
| .getLongestDMRsReplicates | Source code |
| .getSumInRange | Source code |
| .isColor | Source code |
| .isInteger | Source code |
| .joinDMRs | Source code |
| .joinDMRsReplicates | Source code |
| .joinMethylationData | Source code |
| .measureOverlaps | Source code |
| .mergeDMRsIteratively | Source code |
| .mergeDMRsIterativelyReplicates | Source code |
| .mergeRegions | Source code |
| .movingAverage | Source code |
| .movingSum | Source code |
| .plotGeneticElements | Source code |
| .printGenomicRanges | Source code |
| .scoreTest | Source code |
| .smartMergeDMRs | Source code |
| .smartMergeDMRsReplicates | Source code |
| .splitGRangesEqualy | Source code |
| .stopIfNotAll | Source code |
| .suitableForBetaReg | Source code |
| .sumReadsM | Source code Source code |
| .sumReadsM1 | Source code |
| .sumReadsM2 | Source code |
| .sumReadsN | Source code Source code |
| .sumReadsN1 | Source code |
| .sumReadsN2 | Source code |
| .validateConditionReplicates | Source code |
| .validateContext | Source code |
| .validateGRanges | Source code |
| .validateMethylationData | Source code |
| .validateMethylationDataList | Source code |
| .validateMethylationProfile | Source code |
| .validateStatisticalTest | Source code |
| .validateStatisticalTestReplicates | Source code |
| DMRcaller | Man page |
| DMRcaller-package | Man page |
| DMRsNoiseFilterCG | Man page |
| GEs | Man page |
| analyseReadsInsideRegionsForCondition | Man page Source code |
| computeDMRs | Man page Source code |
| computeDMRsReplicates | Man page Source code |
| computeMethylationDataCoverage | Man page Source code |
| computeMethylationDataSpatialCorrelation | Man page Source code |
| computeMethylationProfile | Man page Source code |
| computeOverlapProfile | Man page Source code |
| extractGC | Man page Source code |
| filterDMRs | Man page Source code |
| getWholeChromosomes | Man page Source code |
| joinReplicates | Man page Source code |
| mergeDMRsIteratively | Man page Source code |
| methylationDataList | Man page |
| plotLocalMethylationProfile | Man page Source code |
| plotMethylationDataCoverage | Man page Source code |
| plotMethylationDataSpatialCorrelation | Man page Source code |
| plotMethylationProfile | Man page Source code |
| plotMethylationProfileFromData | Man page Source code |
| plotOverlapProfile | Man page Source code |
| poolMethylationDatasets | Man page Source code |
| poolTwoMethylationDatasets | Man page Source code |
| readBismark | Man page Source code |
| readBismarkPool | Man page Source code |
| saveBismark | Man page Source code |
| syntheticDataReplicates | Man page |
