MethylSeekR: Segmentation of Bis-seq data
Version 1.16.0

This is a package for the discovery of regulatory regions from Bis-seq data

AuthorLukas Burger, Dimos Gaidatzis, Dirk Schubeler and Michael Stadler
Bioconductor views DNAMethylation MethylSeq Sequencing
Date of publicationNone
MaintainerLukas Burger <Lukas.Burger@fmi.ch>
LicenseGPL (>=2)
Version1.16.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("MethylSeekR")

Getting started

Package overview

Popular man pages

MethylSeekR-package: Segmentation of Bis-seq methylation data
plotAlphaDistributionOneChr: Calculate and plot alpha distribution.
plotFinalSegmentation: Plotting final segmentation
readMethylome: Load Bis-seq data
readSNPTable: Load SNP table
removeSNPs: Remove CpGs overlapping SNPs
segmentUMRsLMRs: Identify UMRs and LMRs
See all...

All man pages Function index File listing

Man pages

calculateFDRs: Determine false discovery rate
MethylSeekR-package: Segmentation of Bis-seq methylation data
plotAlphaDistributionOneChr: Calculate and plot alpha distribution.
plotFinalSegmentation: Plotting final segmentation
plotPMDSegmentation: Plotting the PMD Segmentation
readMethylome: Load Bis-seq data
readSNPTable: Load SNP table
removeSNPs: Remove CpGs overlapping SNPs
savePMDSegments: Save PMD segments
saveUMRLMRSegments: Save UMR and LMR segments
segmentPMDs: PMD segmenter
segmentUMRsLMRs: Identify UMRs and LMRs

Functions

MethylSeekR Man page
MethylSeekR-package Man page
PMDviterbiSegmentation Source code
calculateAlphaDistr Source code
calculateFDRs Man page Source code
createGRangesObjectPMDSegmentation Source code
plotAlphaDistributionOneChr Man page Source code
plotFinalSegmentation Man page Source code
plotPMDSegmentation Man page Source code
readMethylome Man page Source code
readSNPTable Man page Source code
removeSNPs Man page Source code
savePMDSegments Man page Source code
saveUMRLMRSegments Man page Source code
segmentPMDs Man page Source code
segmentUMRsLMRs Man page Source code
trainPMDHMM Source code

Files

DESCRIPTION
NAMESPACE
R
R/PMDviterbiSegmentation.R
R/calculateAlphaDistr.R
R/calculateFDRs.R
R/createGRangesObjectPMDSegmentation.R
R/plotAlphaDistributionOneChr.R
R/plotFinalSegmentation.R
R/plotPMDSegmentation.R
R/readMethylome.R
R/readSNPTable.R
R/removeSNPs.R
R/savePMDSegments.R
R/saveUMRLMRSegments.R
R/segmentPMDs.R
R/segmentUMRsLMRs.R
R/trainPMDHMM.R
build
build/vignette.rds
inst
inst/CITATION
inst/doc
inst/doc/MethylSeekR.R
inst/doc/MethylSeekR.Rnw
inst/doc/MethylSeekR.pdf
inst/extdata
inst/extdata/Lister2009_imr90_hg18_chr22.tab
inst/extdata/SNVs_hg18_chr22.tab
man
man/MethylSeekR-package.Rd
man/calculateFDRs.Rd
man/plotAlphaDistributionOneChr.Rd
man/plotFinalSegmentation.Rd
man/plotPMDSegmentation.Rd
man/readMethylome.Rd
man/readSNPTable.Rd
man/removeSNPs.Rd
man/savePMDSegments.Rd
man/saveUMRLMRSegments.Rd
man/segmentPMDs.Rd
man/segmentUMRsLMRs.Rd
vignettes
vignettes/MethylSeekR.Rnw
vignettes/refs.bib
MethylSeekR documentation built on May 20, 2017, 10:15 p.m.

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