Analyze, manage and store whole-genome methylation data

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Documentation for package ‘bsseq’ version 1.44.1

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

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
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
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.
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.bismark	Parsing output from the Bismark alignment suite.
read.modbam2bed	Construct BSseq objects from nanopore BED files
read.modkit	Construct BSseq objects from nanopore BED files
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