# Processing and analyzing bisulfite sequencing data

## Documentation for package ‘BiSeq’ version 1.4.2

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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