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

High-throughput sequencing technologies allow the production of large volumes of short sequences, which can be aligned to the genome to create a set of matches to the genome. By looking for regions of the genome which to which there are high densities of matches, we can infer a segmentation of the genome into regions of biological significance. The methods in this package allow the simultaneous segmentation of data from multiple samples, taking into account replicate data, in order to create a consensus segmentation. This has obvious applications in a number of classes of sequencing experiments, particularly in the discovery of small RNA loci and novel mRNA transcriptome discovery.

AuthorThomas J. Hardcastle
Date of publicationNone
MaintainerThomas J. Hardcastle <tjh48@cam.ac.uk>
LicenseGPL-3
Version2.8.0

View on Bioconductor

Man pages

alignmentClass-class: Class "alignmentClass"

alignmentData-class: Class "alignmentData"

alignmentMeth-class: Class "alignmentMeth"

averageMethylationRegions: Computes and plots the average distribution of aligned reads...

classifySeg: A method for defining a genome segment map by an empirical...

findChunks: Identifies 'chunks' of data within a set of aligned reads.

getCounts: Gets counts from alignment data from a set of genome...

getOverlaps: Identifies overlaps between two sets of genomic coordinates

heuristicSeg: A (fast) heuristic method for creation of a genome segment...

lociData-class: Class "lociData"

lociLikelihoods: Evaluates the posterior likelihoods of each region defined by...

mergeMethSegs: Merges neighbouring methylation loci with the same pattern of...

methData-class: Class "methData"

plotGenome: Plots the alignment of sequence tags on the genome given an...

plotMeth: Plots a map of cytosine methylation (and optionally,...

plotMethDistribution: Plots the distribution of methylation on the genome.

processAD: Processes an 'alignmentData' or 'alignmentMeth' object into a...

readMethods: Functions for processing files of various formats into an...

readMeths: A function for reading data from the YAMA methylation aligner...

segClass-class: Class "segClass"

segData-class: Class "segData"

segmentSeq-package: Segmentation of the genome based on multiple samples of...

segMeth-class: Class "segMeth"

selectLoci: Filters a 'lociData' object based on given selection...

SL: Example data selected from a set of Illumina sequencing...

summariseLoci: Summarise the expected number of loci in a 'lociData' object.

Files in this package

segmentSeq/DESCRIPTION
segmentSeq/NAMESPACE
segmentSeq/R
segmentSeq/R/AllClasses.R segmentSeq/R/alignmentClass-accessors.R segmentSeq/R/alignmentData-accessors.R segmentSeq/R/alignmentMeth-accessors.R segmentSeq/R/classifySeg.R segmentSeq/R/constructNulls.R segmentSeq/R/findChunks.R segmentSeq/R/getCounts.R segmentSeq/R/getOverlaps.R segmentSeq/R/heuristicSeg.R segmentSeq/R/lociData-accessors.R segmentSeq/R/lociLikelihoods.R segmentSeq/R/mergeSegs.R segmentSeq/R/methData-accessors.R segmentSeq/R/plotGenome.R segmentSeq/R/plotGenomicDistributions.R segmentSeq/R/processAD.R segmentSeq/R/processPosteriors.R segmentSeq/R/processTags.R segmentSeq/R/segClass-accessors.R segmentSeq/R/segData-accessors.R segmentSeq/R/segMeth-accessors.R segmentSeq/R/selectLoci.R segmentSeq/R/utilityFunctions.R
segmentSeq/build
segmentSeq/build/vignette.rds
segmentSeq/inst
segmentSeq/inst/doc
segmentSeq/inst/doc/methylationAnalysis.R
segmentSeq/inst/doc/methylationAnalysis.Rnw
segmentSeq/inst/doc/methylationAnalysis.pdf
segmentSeq/inst/doc/segmentSeq.R
segmentSeq/inst/doc/segmentSeq.Rnw
segmentSeq/inst/doc/segmentSeq.pdf
segmentSeq/inst/extdata
segmentSeq/inst/extdata/SL10.txt
segmentSeq/inst/extdata/SL26.txt
segmentSeq/inst/extdata/SL32.txt
segmentSeq/inst/extdata/SL9.txt
segmentSeq/inst/extdata/short_13_C24_col_trim.fastq_CG_methCalls.gz
segmentSeq/inst/extdata/short_18B_C24_C24_trim.fastq_CG_methCalls.gz
segmentSeq/inst/extdata/short_Sample_17A_trimmed.fastq_CG_methCalls.gz
segmentSeq/inst/extdata/short_Sample_28_trimmed.fastq_CG_methCalls.gz
segmentSeq/man
segmentSeq/man/SL.Rd segmentSeq/man/alignmentClass-class.Rd segmentSeq/man/alignmentData-class.Rd segmentSeq/man/alignmentMeth-class.Rd segmentSeq/man/averageMethylationRegions.Rd segmentSeq/man/classifySeg.Rd segmentSeq/man/findChunks.Rd segmentSeq/man/getCounts.Rd segmentSeq/man/getOverlaps.Rd segmentSeq/man/heuristicSeg.Rd segmentSeq/man/lociData-class.Rd segmentSeq/man/lociLikelihoods.Rd segmentSeq/man/mergeMethSegs.Rd segmentSeq/man/methData-class.Rd segmentSeq/man/plotGenome.Rd segmentSeq/man/plotMeth.Rd segmentSeq/man/plotMethDistribution.Rd segmentSeq/man/processAD.Rd segmentSeq/man/readMethods.Rd segmentSeq/man/readMeths.Rd segmentSeq/man/segClass-class.Rd segmentSeq/man/segData-class.Rd segmentSeq/man/segMeth-class.Rd segmentSeq/man/segmentSeq-package.Rd segmentSeq/man/selectLoci.Rd segmentSeq/man/summariseLoci.Rd
segmentSeq/vignettes
segmentSeq/vignettes/methylationAnalysis.Rnw
segmentSeq/vignettes/segmentSeq.Rnw

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