segmentSeq
Methods for identifying small RNA loci from high-throughput sequencing data

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Search the segmentSeq package
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Functions
166
Source code
27
Man pages
30
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segmentSeq: Methods for identifying small RNA loci from high-throughput sequencing data
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API

API for segmentSeq
Methods for identifying small RNA loci from high-throughput sequencing data

Global functions
.DF2matrix Source code
.chrProcessing Source code
.classifyLoci Source code
.classifyNulls Source code
.constructMethNulls Source code
.constructNullPriors Source code
.constructNulls Source code
.constructPriorNulls Source code
.controlFDR Source code
.controlFWER Source code
.convertSegToLoci Source code
.extractStrand Source code
.fastUniques Source code Source code
.filterChunks Source code
.filterSegments Source code
.findMethChunks Source code
.getCounts Source code
.getLocLikelihoods Source code
.getMethylatedCounts Source code
.getOverlaps Source code
.inferMethNulls Source code
.inferNulls Source code
.lociLikelihoods Source code
.massiveClassifyLoci Source code
.massiveClassifyNulls Source code
.matrix2Rle Source code
.mergeListLoci Source code
.mergeSegData Source code
.methFunction Source code
.methLikelihoods Source code
.partheuristicSeg Source code
.plotSampleMeth Source code
.printIRangesMatrix Source code
.printLocLikes Source code
.processPosteriors Source code
.processPosts Source code
.processTags Source code
.rowSumDF Source code
.splitSD Source code
.squeezeAlign Source code
.subProfile Source code
.tagDuplicated Source code
.trimMeth Source code
.valid.alignmentClass Source code
.windowing Source code
.zeroInMeth Source code
SL10 Man page
SL26 Man page
SL32 Man page
SL9 Man page
[,alignmentClass,ANY,ANY,ANY-method Man page
[,alignmentClass,ANY,ANY-method Man page
[,alignmentClass,ANY-method Man page
[,alignmentClass-method Man page
[,alignmentData,ANY,ANY,ANY-method Man page
[,alignmentData,ANY,ANY-method Man page
[,alignmentData,ANY-method Man page
[,alignmentData-method Man page
[,alignmentMeth,ANY,ANY,ANY-method Man page
[,alignmentMeth,ANY,ANY-method Man page
[,alignmentMeth,ANY-method Man page
[,alignmentMeth-method Man page
[,lociData,ANY,ANY,ANY-method Man page
[,lociData,ANY,ANY-method Man page
[,lociData,ANY-method Man page
[,lociData-method Man page
[,methData,ANY,ANY,ANY-method Man page
[,methData,ANY,ANY-method Man page
[,methData,ANY-method Man page
[,methData-method Man page
[,segClass,ANY,ANY-method Man page
[,segClass-method Man page
[,segData,ANY,ANY-method Man page
[,segData,ANY-method Man page
[,segData-method Man page
[,segMeth,ANY,ANY-method Man page
[,segMeth,ANY-method Man page
[,segMeth-method Man page
alignmentClass Man page
alignmentClass-class Man page
alignmentData Man page
alignmentData-class Man page
alignmentMeth Man page
alignmentMeth-class Man page
averageProfiles Man page Source code
c,lociData-method Man page
cbind,alignmentClass-method Man page
cbind,alignmentData-method Man page
cbind,alignmentMeth-method Man page
classifySeg Man page Source code
dim,alignmentClass-method Man page
dim,alignmentData-method Man page
dim,alignmentMeth-method Man page
dim,lociData-method Man page
dim,methData-method Man page
dim,segClass-method Man page
dim,segData-method Man page
dim,segMeth-method Man page
findChunks Man page Source code
getCounts Man page Source code
getOverlaps Man page Source code
givenExpression Man page Source code
hSL Man page
heuristicSeg Man page Source code
initialize,alignmentClass-method Man page
initialize,alignmentData-method Man page
initialize,alignmentMeth-method Man page
initialize,segClass-method Man page
initialize,segData-method Man page
initialize,segMeth-method Man page
lociData Man page
lociData-class Man page
lociLikelihoods Man page Source code
mergeMethSegs Man page Source code
methData Man page
methData-class Man page
normaliseNC Man page Source code
plotAverageProfile Man page Source code
plotGenome Man page Source code
plotMeth Man page Source code
plotMethDistribution Man page Source code
processAD Man page Source code
readBAM Man page Source code
readGeneric Man page Source code
readMeths Man page Source code
segClass Man page
segClass-class Man page
segData Man page
segData-class Man page
segMeth Man page
segMeth-class Man page
segmentSeq Man page
segmentSeq-package Man page
selectLoci Man page Source code
show,alignmentClass-method Man page
show,alignmentData-method Man page
show,alignmentMeth-method Man page
show,lociData-method Man page
show,methData-method Man page
show,segClass-method Man page
show,segData-method Man page
show,segMeth-method Man page
summariseLoci Man page Source code
thresholdFinder Man page Source code
segmentSeq documentation built on Nov. 8, 2020, 5:18 p.m.

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