Processing and analyzing bisulfite sequencing data

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Documentation for package ‘BiSeq’ version 1.40.0

• 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