Differentially Methylated Regions Caller

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Documentation for package ‘DMRcaller’ version 1.45.3

• DESCRIPTION file
• User guides, package vignettes and other documentation
• Package NEWS

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A C D E F G J M O P R S misc

DMRcaller-package

Call Differentially Methylated Regions (DMRs) between two samples

-- A --

analyseReadsInsideRegionsForCondition	Analyse reads inside regions for condition
analyseReadsInsideRegionsForConditionPMD	Analyse reads inside regions for condition

-- C --

computeCoMethylatedPositions	Compute pairwise co-methylation statistics for cytosine sites within regions
computeCoMethylatedRegions	Compute pairwise co-methylation statistics between regions
computeDMRs	Compute DMRs
computeDMRsReplicates	Compute DMRs
computeMethylationDataCoverage	Compute methylation data coverage
computeMethylationDataSpatialCorrelation	Compute methylation data spatial correlation
computeMethylationProfile	Compute methylation profile
computeOverlapProfile	Compute Overlaps Profile
computePMDs	Compute PMDs
computeVMDs	Compute VMDs

-- D --

DMRcaller	Call Differentially Methylated Regions (DMRs) between two samples
DMRsNoiseFilterCG	The DMRs between WT and met1-3 in CG context

-- E --

extractGC

Extract GC

-- F --

filterDMRs	Filter DMRs
filterPMDs	Filter PMDs
filterVMDs	Filter VMDs
filterVMRsONT	Filter VMRs for ONT Data

-- G --

GEs	The genetic elements data
GEs_hg38	The genetic elements data of GRCh38 Genome Reference
getWholeChromosomes	Get whole chromosomes from methylation data

-- J --

joinReplicates

Joins together two GRange objects in a single containing all the replicates

-- M --

mergeDMRsIteratively	Merge DMRs iteratively
mergePMDsIteratively	Merge PMDs iteratively
methylationDataList	The methylation data list

-- O --

ontSampleGRangesList	The ONT methylation data list
ont_gr_GM18870_chr1_PMD_bins_1k	Partially Methilated Domains example
ont_gr_GM18870_chr1_sorted_bins_1k	The ONT methylation data example

-- P --

plotLocalMethylationProfile	Plot local methylation profile
plotMethylationDataCoverage	Plot methylation data coverage
plotMethylationDataSpatialCorrelation	Plot methylation data spatial correlation
plotMethylationProfile	Plot Methylation Profile
plotMethylationProfileFromData	Plot methylation profile from data
plotOverlapProfile	Plot overlap profile
PMDsBinsCG	The PMDs between GM18501 and GM18876 using Bins method
PMDsNoiseFilterCG	The PMDs between GM18501 and GM18876 using Noise_filter method
poolMethylationDatasets	Pool methylation data
poolTwoMethylationDatasets	Pool two methylation datasets

-- R --

readBismark	Read Bismark
readBismarkPool	Read Bismark pool
readONTbam	Load ONT BAM, decode MM/ML, and count modified vs. unmodified reads

-- S --

saveBismark	Save Bismark
scanBamChr1Random5	The bam file from ONT nanopore .pod5 files
selectCytosine	Select Cytosine Positions
syntheticDataReplicates	Simulated data for biological replicates

-- misc --

.analyseReadsInsideBins	Analyse reads inside regions
.analyseReadsInsideBinsOneSample	Analyse reads inside regions for one sample
.analyseReadsInsideBinsPMDs	Analyse reads inside regions
.analyseReadsInsideBinsReplicates	Analyse reads inside regions
.analyseReadsInsideRegions	Analyse reads inside regions
.analyseReadsInsideRegionsForCondition	Analyse reads inside regions
.analyseReadsInsideRegionsOneSample	Analyse reads inside regions
.analyseReadsInsideRegionsPMDs	Analyse reads inside regions
.analyseReadsInsideRegionsReplicates	Analyse reads inside regions
.analyseReadsInsideRegionsVMDs	Analyse reads inside regions with computing mean and standard deviation per-read proportions
.analyseReadsInsideRegionsVMR	Analyse reads inside regions (with VMR testing)
.computeaAjustedPValuesInDMRs	Compute adjusted p-values in DMRs
.computeaAjustedPValuesInDMRsReplicates	Compute adjusted p-values
.computeAdjuestedPValues	Compute adjusted p-values
.computeAdjuestedPValuesReplicates	Compute adjusted p-values
.computeBetaReg	This function applies the .computeBetaRegSingle to the entire dataset
.computeBetaRegSingle	Beta regression
.computeDMRsBins	This function computes the differentially methylated regions between two conditions using the bins method.
.computeDMRsNeighbourhood	This function computes the differentially methylated regions between two conditions using the neighbourhood method. This assumes the computation of differentially methylated cytosines followed by smart merging of these cytosines while keeping the new DMRs statistically significant.
.computeDMRsNoiseFilter	This function computes the differentially methylated regions between two conditions using the noise filter method.
.computeDMRsReplicatesBins	This function computes the differentially methylated regions between replicates using the bins method.
.computeDMRsReplicatesNeighbourhood	This function computes the differentially methylated regions between replicates using the neighbourhood method.
.computeMethylationDataSpatialCorrelation	Compute methylation data spatial correlation
.computePMDsBins	This function computes the partially methylated regions using the bins method.
.computePMDsNeighbourhood	This function computes the partially methylated domains using the neighbourhood method. This assumes the computation of partially methylated cytosines followed by smart merging of these cytosines while keeping the new PMDs statistically significant.
.computePMDsNoiseFilter	This function computes the partially methylated regions using the noise filter method.
.computeProportionsInDMRs	This function recalculate proportions between methylated and total reads in a new region.
.computeVMDsBins	This function computes the variance methylated regions using the bins method.
.convertResult	This function extracts the p-value for each cytosine from the betareg object
.countCytosinesInside	Count cytosines inside
.countMethylationDataCoverage	Count methylation data coverage
.countTotalNumberOfCytosines	Count total number of Cytosines
.fisherTest	Fisher test
.fisherTestPValue	Fisher test
.isColor	Is color
.isInteger	.is.integer
.joinMethylationData	Join methylation data
.mergeDMRsIteratively	This takes a list of DMRs and attempts to merge DMRs while keeping the new DMRs statistically significant
.mergePMDsIteratively	This takes a list of PMDs and attempts to merge PMDs while keeping the new PMDs filtering by the preset parameter
.movingAverage	Moving average
.movingSum	Moving sum
.plotGeneticElements	Plot genetic elements
.printGenomicRanges	Print GenomicRanges
.scoreTest	Score test
.smartMergeDMRs	This takes a list of DMRs and attempts to merge DMRs while keeping the new DMRs statistically significant
.smartMergeDMRsReplicates	This takes a list of DMRs and attempts to merge DMRs while keeping the new DMRs statistically significant
.smartMergePMDs	This takes a list of PMDs and attempts to merge PMDs while keeping the new PMDs statistically significant
.splitGRangesEqualy	.splitGRangesEqualy
.stopIfNotAll	.stopIfNotAll
.validateConditionReplicates	Validate the condition of the experiment
.validateGRanges	Validate GRanges
.validateMethylationData	Validate methylation data
.validateMethylationDataList	Validate methylation data
.validateMethylationProfile	Validate methylation profile
.validateModif	Validate Modification Tag in BAM
.validateStatisticalTest	Validate statistial test
.validateStatisticalTestReplicates	Validate statistial test