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

alignmentClass-classClass "alignmentClass"
alignmentData-classClass "alignmentData"
alignmentMeth-classClass "alignmentMeth"
averageMethylationRegionsComputes and plots the average distribution of aligned reads...
classifySegA method for defining a genome segment map by an empirical...
findChunksIdentifies 'chunks' of data within a set of aligned reads.
getCountsGets counts from alignment data from a set of genome...
getOverlapsIdentifies overlaps between two sets of genomic coordinates
givenExpressionAdjusts posterior likelihoods of differential expression by...
heuristicSegA (fast) heuristic method for creation of a genome segment...
hSLPreprocessed 'lociData' object containing likelihoods of...
lociData-classClass "lociData"
lociLikelihoodsEvaluates the posterior likelihoods of each region defined by...
mergeMethSegsMerges neighbouring methylation loci with the same pattern of...
methData-classClass "methData"
normaliseNCA function providing adjustment of cytosine...
plotGenomePlots the alignment of sequence tags on the genome given an...
plotMethPlots a map of cytosine methylation (and optionally,...
plotMethDistributionPlots the distribution of methylation on the genome.
processADProcesses an 'alignmentData' or 'alignmentMeth' object into a...
readMethodsFunctions for processing files of various formats into an...
readMethsA function for reading data from the YAMA methylation aligner...
segClass-classClass "segClass"
segData-classClass "segData"
segmentSeq-packageSegmentation of the genome based on multiple samples of...
segMeth-classClass "segMeth"
selectLociFilters a 'lociData' object based on given selection...
SLExample data selected from a set of Illumina sequencing...
summariseLociSummarise the expected number of loci in a 'lociData' object.
thresholdFinderDetermines threshold for the proportion of methylation at...
segmentSeq documentation built on May 2, 2018, 4:12 a.m.