DMRcate: Methylation array and sequencing spatial analysis methods
Version 1.12.0

De novo identification and extraction of differentially methylated regions (DMRs) from the human genome using Whole Genome Bisulphite Sequencing (WGBS) and Illumina Infinium Array (450K and EPIC) data. Provides functionality for filtering probes possibly confounded by SNPs and cross-hybridisation. Includes GRanges generation and plotting functions.

AuthorTim Peters
Bioconductor views DNAMethylation DifferentialExpression DifferentialMethylation GeneExpression Genetics GenomeAnnotation MethylationArray Microarray MultipleComparison OneChannel QualityControl TimeCourse TwoChannel
Date of publicationNone
MaintainerTim Peters <t.peters@garvan.org.au>
Licensefile LICENSE
Version1.12.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("DMRcate")

Getting started

Package overview

Popular man pages

cpg.annotate: Annotate CpGs with their chromosome position and test...
dmrcate: DMR identification
DMRcate-internal: Internal DMRcate objects and functions
DMRcate-package: DMR calling from bisulphite sequencing and Illumina array...
DMR.plot: Plotting DMRs
extractRanges: Create GRanges object from 'dmrcate' output.
rmSNPandCH: Filter probes
See all...

All man pages Function index File listing

Man pages

cpg.annotate: Annotate CpGs with their chromosome position and test...
dmrcate: DMR identification
DMRcate-internal: Internal DMRcate objects and functions
DMRcate-package: DMR calling from bisulphite sequencing and Illumina array...
DMR.plot: Plotting DMRs
extractRanges: Create GRanges object from 'dmrcate' output.
rmSNPandCH: Filter probes

Functions

Files

DESCRIPTION
LICENSE
NAMESPACE
NEWS
R
R/DMR.plot.R
R/KernelSums.R
R/KernelTest.R
R/SparseDeltas.R
R/cpg.annotate.R
R/dmrcate.R
R/extractCoords.R
R/extractRanges.R
R/fitParallel.R
R/rmSNPandCH.R
build
build/vignette.rds
data
inst
inst/CITATION
inst/doc
inst/doc/DMRcate.R
inst/doc/DMRcate.Rnw
inst/doc/DMRcate.pdf
inst/unitTests
inst/unitTests/test_pipeline.R
man
man/DMR.plot.Rd
man/DMRcate-internal.Rd
man/DMRcate-package.Rd
man/cpg.annotate.Rd
man/dmrcate.Rd
man/extractRanges.Rd
man/rmSNPandCH.Rd
tests
tests/runTests.R
vignettes
vignettes/DMRcate.Rnw
vignettes/heynSNP.pdf
DMRcate documentation built on May 20, 2017, 9:25 p.m.

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