annotateGRanges | Annotates a 'GRanges' object by means of a second 'GRanges' object |
annotateGRanges-method | Annotates a 'GRanges' object by means of a second 'GRanges' object |
betaRegression | A function to estimate and test a group factor within a beta regression |
betaRegression-method | A function to estimate and test a group factor within a beta regression |
betaResults | The output of 'betaRegression' |
betaResultsNull | The output of 'betaRegression' for resampled data |
binomLikelihoodSmooth | Calculates local likelihood estimations for binomial random variables |
binomLikelihoodSmooth-method | Calculates local likelihood estimations for binomial random variables |
BSraw | Class to contain raw Bisulfite Sequencing (BiSeq) Data |
BSraw-class | Class to contain raw Bisulfite Sequencing (BiSeq) Data |
BSraw-method | Class to contain raw Bisulfite Sequencing (BiSeq) Data |
BSrel | Class to contain Bisulfite Sequencing (BiSeq) Data |
BSrel-class | Class to contain Bisulfite Sequencing (BiSeq) Data |
BSrel-method | Class to contain Bisulfite Sequencing (BiSeq) Data |
clusterSites | Assigns CpG cluster memberships on CpG sites within 'BSraw' objects |
clusterSites-method | Assigns CpG cluster memberships on CpG sites within 'BSraw' objects |
clusterSitesToGR | A function to obtain a 'GRanges' object of CpG clusters from 'BSraw' and 'BSrel' objects |
clusterSitesToGR-method | A function to obtain a 'GRanges' object of CpG clusters from 'BSraw' and 'BSrel' objects |
combine-method | Class to contain raw Bisulfite Sequencing (BiSeq) Data |
combine-method | Class to contain Bisulfite Sequencing (BiSeq) Data |
compareTwoSamples | Detects DMRs by comparing two samples |
compareTwoSamples-method | Detects DMRs by comparing two samples |
covBoxplots | Creates boxplots of coverages per sample |
covBoxplots-method | Creates boxplots of coverages per sample |
covStatistics | Prints a short summary of coverage statistics per sample |
covStatistics-method | Prints a short summary of coverage statistics per sample |
DMRs | The output of 'findDMRs' |
estLocCor | Estimates the correlations of the z-scores |
estLocCor-method | Estimates the correlations of the z-scores |
filterByCov | Filters regions (or single CpGs) of a 'BSraw' object with a minimum coverage |
filterByCov-method | Filters regions (or single CpGs) of a 'BSraw' object with a minimum coverage |
filterBySharedRegions | Reduces a 'BSraw' or 'BSrel' object to regions (or single CpGs) shared by a fraction of samples |
filterBySharedRegions-method | Reduces a 'BSraw' or 'BSrel' object to regions (or single CpGs) shared by a fraction of samples |
findDMRs | Aggregates CpG sites to DMRs |
findDMRs-method | Aggregates CpG sites to DMRs |
globalTest | Test whether at least one CpG is differentially methylated in a given genomic region |
globalTest-method | Test whether at least one CpG is differentially methylated in a given genomic region |
limitCov | Limits the coverage of a 'BSraw' object |
limitCov-method | Limits the coverage of a 'BSraw' object |
logisticRegression | Estimates and tests a group factor |
logisticRegression-method | Estimates and tests a group factor |
makeVariogram | Variogram estimator. |
makeVariogram-method | Variogram estimator. |
methLevel | Class to contain Bisulfite Sequencing (BiSeq) Data |
methLevel-method | Class to contain Bisulfite Sequencing (BiSeq) Data |
methLevel<- | Class to contain Bisulfite Sequencing (BiSeq) Data |
methLevel<--method | Class to contain Bisulfite Sequencing (BiSeq) Data |
methReads | Class to contain raw Bisulfite Sequencing (BiSeq) Data |
methReads-method | Class to contain raw Bisulfite Sequencing (BiSeq) Data |
methReads<- | Class to contain raw Bisulfite Sequencing (BiSeq) Data |
methReads<--method | Class to contain raw Bisulfite Sequencing (BiSeq) Data |
plotBindingSites | Plots the mean methylation of given regions |
plotBindingSites-method | Plots the mean methylation of given regions |
plotMeth | Plots raw and smoothed methylation data for a given region |
plotMeth-method | Plots raw and smoothed methylation data for a given region |
plotMethMap | Plots methylation values of multiple samples in a given region |
plotMethMap-method | Plots methylation values of multiple samples in a given region |
plotSmoothMeth | Plots smoothed methylation values for a bunch of samples and a given region |
plotSmoothMeth-method | Plots smoothed methylation values for a bunch of samples and a given region |
predictedMeth | The output of 'predictMeth' |
predictMeth | Predicts methylation levels along CpG sites or for a grid of sites in CpG clusters. |
predictMeth-method | Predicts methylation levels along CpG sites or for a grid of sites in CpG clusters. |
promoters | A 'GRanges' of promoters of the human genome |
rawToRel | Converts a 'BSraw' object to a 'BSrel' object |
rawToRel-method | Converts a 'BSraw' object to a 'BSrel' object |
readBismark | Reads cytosine methylation stati determined by Bismark |
readBismark-method | Reads cytosine methylation stati determined by Bismark |
rrbs | RRBS data of APL patient samples and controls. |
smoothVariogram | Smoothes variogram |
smoothVariogram-method | Smoothes variogram |
summarizeRegions | Aggregates methylation information of single CpG sites |
summarizeRegions-method | Aggregates methylation information of single CpG sites |
testClusters | Tests CpG clusters |
testClusters-method | Tests CpG clusters |
totalReads | Class to contain raw Bisulfite Sequencing (BiSeq) Data |
totalReads-method | Class to contain raw Bisulfite Sequencing (BiSeq) Data |
totalReads<- | Class to contain raw Bisulfite Sequencing (BiSeq) Data |
totalReads<--method | Class to contain raw Bisulfite Sequencing (BiSeq) Data |
trimClusters | Trims CpG clusters |
trimClusters-method | Trims CpG clusters |
vario | Output of 'makeVariogram' |
writeBED | Writes 'BSraw' and 'BSrel' data to a bed file suitable for the IGV |
writeBED-method | Writes 'BSraw' and 'BSrel' data to a bed file suitable for the IGV |