Analyze, manage and store bisulfite sequencing data


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Documentation for package ‘bsseq’ version 1.12.2

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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
collapseBSseq Class BSseq
combine-method Class BSseq
combineList Class BSseq
data.frame2GRanges Converts a data frame to a GRanges.
dmrFinder Finds differentially methylated regions for whole genome bisulfite sequencing data.
end-method Class hasGRanges
end<--method Class hasGRanges
findOverlaps-method Class hasGRanges
fisherTests Compute Fisher-tests for a BSseq object
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 Class hasGRanges
length-method Class BSseq
length-method Class hasGRanges
orderBSseq Class BSseq
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.bsmooth Parsing output from the BSmooth alignment suite
read.umtab Parsing UM tab files (legacy output) containing output from the BSmooth aligner.
read.umtab2 Parsing UM tab files (legacy output) containing output from the BSmooth aligner.
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 Class hasGRanges
seqnames<--method Class hasGRanges
show-method Class BSseq
show-method Class BSseqStat
show-method Class BSseqTstat
start-method Class hasGRanges
start<--method Class hasGRanges
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 Class hasGRanges
width<--method Class hasGRanges
[-method Class BSseq
[-method Class BSseqStat
[-method Class BSseqTstat
[-method Class hasGRanges