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

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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.

Author
Thomas J. Hardcastle
Date of publication
None
Maintainer
Thomas J. Hardcastle <tjh48@cam.ac.uk>
License
GPL-3
Version
2.8.0

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