# Analyze, manage and store whole-genome methylation data

## Documentation for package ‘bsseq’ version 1.49.0

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

## Help Pages

assayNames-method | Class BSseq
assays-method | Class BSseq
binomialGoodnessOfFit | Binomial and poisson goodness of fit statistics for BSSeq objects
BS.chr22 | Whole-genome bisulfite sequencing for chromosome 22 from Lister et al.
BSmooth | BSmooth, smoothing bisulfite sequence data
BSmooth.tstat | Compute t-statistics based on smoothed whole-genome bisulfite sequencing data.
BSseq | The constructor function for BSseq objects.
BSseq-class | Class BSseq
bsseq-deprecated | Deprecated functions in package 'bsseq'
BSseqStat | Class BSseqStat
BSseqStat-class | Class BSseqStat
BSseqTstat | Class BSseqTstat
BSseqTstat-class | Class BSseqTstat
chisqGoodnessOfFit | Binomial and poisson goodness of fit statistics for BSSeq objects
chrSelectBSseq | Class BSseq
class:hasGRanges | Class hasGRanges
collapseBSseq | Class BSseq
combine-method | Class BSseq
combineList | Class BSseq
data.frame2GRanges | Converts a data frame to a GRanges.
dimnames-method | Classes FWIRanges and FWGRanges
dmrFinder | Finds differentially methylated regions for whole genome bisulfite sequencing data.
end-method | Classes FWIRanges and FWGRanges
end-method | Class hasGRanges
end<--method | Classes FWIRanges and FWGRanges
end<--method | Class hasGRanges
estimateErrorRate | Estimate CpG-specific error rate from BSseq object.
findLoci | Find methylation loci in a genome
findOverlaps-method | Classes FWIRanges and FWGRanges
findOverlaps-method | Class hasGRanges
fisherTests | Compute Fisher-tests for a BSseq object
FWGRanges-class | Classes FWIRanges and FWGRanges
FWIRanges-class | Classes FWIRanges and FWGRanges
getBSseq | Class BSseq
getCoverage | Obtain coverage for BSseq objects.
getCpGMatrix | Generate a matrix of the most likely CpG status for a multi-sample BSseq object.
getCpGs | Get CpG (and non-CpG) loci from a single sample BSseq object.
getMaxLikelihoodMatrix | Generate a matrix of the scaled likelihood of most likely CpG status for a multi-sample BSseq object.
getMeth | Obtain methylation estimates for BSseq objects.
getStats | Obtain statistics from a BSseqTstat object
granges-method | Class hasGRanges
hasBeenSmoothed | Class BSseq
hasGRanges | Class hasGRanges
hasGRanges-class | Class hasGRanges
length-method | Class BSseq
length-method | Class hasGRanges
names-method | Classes FWIRanges and FWGRanges
names<--method | Classes FWIRanges and FWGRanges
orderBSseq | Class BSseq
overlapsAny-method | Class hasGRanges
pData-method | Class BSseq
pData<--method | Class BSseq
plot.chisqGoodnessOfFit | Binomial and poisson goodness of fit statistics for BSSeq objects
plotManyRegions | Plotting BSmooth methylation estimates
plotRegion | Plotting BSmooth methylation estimates
poissonGoodnessOfFit | Binomial and poisson goodness of fit statistics for BSSeq objects
print.chisqGoodnessOfFit | Binomial and poisson goodness of fit statistics for BSSeq objects
read.bedMethyl | Parsing bedMethyl output from modkit pileup.
read.bismark | Parsing output from the Bismark alignment suite.
sampleNames-method | Class BSseq
sampleNames<--method | Class BSseq
seqlengths-method | Class hasGRanges
seqlengths<--method | Class hasGRanges
seqlevels-method | Class hasGRanges
seqlevels<--method | Class hasGRanges
seqnames-method | Classes FWIRanges and FWGRanges
seqnames-method | Class hasGRanges
seqnames<--method | Class hasGRanges
show-method | Class BSseq
show-method | Class BSseqStat
show-method | Class BSseqTstat
start-method | Classes FWIRanges and FWGRanges
start-method | Class hasGRanges
start<--method | Classes FWIRanges and FWGRanges
start<--method | Class hasGRanges
strand-method | Classes FWIRanges and FWGRanges
strand-method | Class hasGRanges
strand<--method | Class hasGRanges
strandCollapse | Class BSseq
subsetByOverlaps-method | Class hasGRanges
updateObject-method | Class BSseq
updateObject-method | Class BSseqStat
updateObject-method | Class BSseqTstat
width-method | Classes FWIRanges and FWGRanges
width-method | Class hasGRanges
width<--method | Classes FWIRanges and FWGRanges
width<--method | Class hasGRanges
[-method | Class BSseq
[-method | Class BSseqStat
[-method | Class BSseqTstat
[-method | Class hasGRanges