Processing and analyzing bisulfite sequencing data


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Documentation for package ‘BiSeq’ version 1.4.2

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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