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

Global functions
DF2matrix 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
averageMethylationRegions Source code
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
chrProcessing Source code
classifyLoci Source code
classifyNulls Source code
classifySeg Man page Source code
constructMethNulls Source code
constructNullPriors Source code
constructNulls Source code
constructPriorNulls Source code
controlFDR Source code
controlFWER Source code
convertSegToLoci 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
extractStrand Source code
fastUniques Source code Source code
filterChunks Source code
filterSegments Source code
findChunks Man page Source code
findMethChunks Source code
getCounts Man page Source code Source code
getLocLikelihoods Source code
getMethylatedCounts Source code
getOverlaps Man page Source code 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 Source code
massiveClassifyLoci Source code
massiveClassifyNulls Source code
matrix2Rle Source code
mergeListLoci Source code
mergeMethSegs Man page Source code
mergeSegData Source code
methData Man page
methData-class Man page
methFunction Source code
methLikelihoods Source code
nferMethNulls Source code
nferNulls Source code
normaliseNC Man page Source code
partheuristicSeg Source code
plotAverageProfile Man page Source code
plotGenome Man page Source code
plotMeth Man page Source code
plotMethDistribution Man page Source code
plotSampleMeth Source code
printIRangesMatrix Source code
printLocLikes Source code
processAD Man page Source code
processPosteriors Source code
processPosts Source code
processTags Source code
readBAM Man page Source code
readGeneric Man page Source code
readMeths Man page Source code
rowSumDF 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
splitSD Source code
squeezeAlign Source code
subProfile Source code
summariseLoci Man page Source code
tagDuplicated Source code
thresholdFinder Man page Source code
trimMeth Source code
valid.alignmentClass Source code
windowing Source code
zeroInMeth Source code
segmentSeq documentation built on Nov. 17, 2017, 8:51 a.m.