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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("segmentSeq")
AuthorThomas J. Hardcastle
Bioconductor views Alignment DataImport DifferentialExpression MultipleComparison QualityControl Sequencing
Date of publicationNone
MaintainerThomas J. Hardcastle <tjh48@cam.ac.uk>
LicenseGPL-3
Version2.10.0

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...

givenExpression: Adjusts posterior likelihoods of differential expression by...

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

hSL: Preprocessed 'lociData' object containing likelihoods of...

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"

normaliseNC: A function providing adjustment of cytosine...

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.

thresholdFinder: Determines threshold for the proportion of methylation at...

Functions

alignmentClass Man page
[,alignmentClass,ANY,ANY,ANY-method Man page
[,alignmentClass,ANY,ANY-method Man page
[,alignmentClass,ANY-method Man page
alignmentClass-class Man page
[,alignmentClass-method Man page
alignmentData Man page
[,alignmentData,ANY,ANY,ANY-method Man page
[,alignmentData,ANY,ANY-method Man page
[,alignmentData,ANY-method Man page
alignmentData-class Man page
[,alignmentData-method Man page
alignmentMeth Man page
[,alignmentMeth,ANY,ANY,ANY-method Man page
[,alignmentMeth,ANY,ANY-method Man page
[,alignmentMeth,ANY-method Man page
alignmentMeth-class Man page
[,alignmentMeth-method Man page
averageProfiles Man page
cbind,alignmentClass-method Man page
cbind,alignmentData-method Man page
cbind,alignmentMeth-method Man page
classifySeg Man page
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
getCounts Man page
givenExpression Man page
heuristicSeg Man page
hSL Man page
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,ANY,ANY,ANY-method Man page
[,lociData,ANY,ANY-method Man page
[,lociData,ANY-method Man page
lociData-class Man page
[,lociData-method Man page
lociLikelihoods Man page
mergeMethSegs Man page
methData Man page
[,methData,ANY,ANY,ANY-method Man page
[,methData,ANY,ANY-method Man page
[,methData,ANY-method Man page
methData-class Man page
[,methData-method Man page
normaliseNC Man page
plotAverageProfile Man page
plotGenome Man page
plotMeth Man page
plotMethDistribution Man page
processAD Man page
readBAM Man page
readGeneric Man page
readMeths Man page
segClass Man page
[,segClass,ANY,ANY-method Man page
segClass-class Man page
[,segClass-method Man page
segData Man page
[,segData,ANY,ANY-method Man page
[,segData,ANY-method Man page
segData-class Man page
[,segData-method Man page
segmentSeq Man page
segmentSeq-package Man page
segMeth Man page
[,segMeth,ANY,ANY-method Man page
[,segMeth,ANY-method Man page
segMeth-class Man page
[,segMeth-method Man page
selectLoci Man page
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
SL10 Man page
SL26 Man page
SL32 Man page
SL9 Man page
summariseLoci Man page
thresholdFinder Man page

Files

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

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