ARRmNormalization: Adaptive Robust Regression normalization for Illumina methylation data
Version 1.16.0

Perform the Adaptive Robust Regression method (ARRm) for the normalization of methylation data from the Illumina Infinium HumanMethylation 450k assay.

AuthorJean-Philippe Fortin, Celia M.T. Greenwood, Aurelie Labbe.
Bioconductor views DNAMethylation Microarray Preprocessing TwoChannel
Date of publicationNone
MaintainerJean-Philippe Fortin <jfortin@jhsph.edu>
LicenseArtistic-2.0
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("ARRmNormalization")

Getting started

Package overview

Popular man pages

ARRmNormalization-package: ARRm normalization for Illumina methylation data
getCoefficients: Return the coefficients from the ARRm linear model
getDesignInfo: Build the chip and position indices
normalizeARRm: Perform ARRm normalization
positionPlots: Plots to evalue chip position effects on different...
ProbesType: Probe Design information for the 450k methylation assay
quantilePlots: Diagnostic plots for evaluation of background effects and dye...
See all...

All man pages Function index File listing

Man pages

ARRmNormalization-internal: Internal ARRmNormalization Functions
ARRmNormalization-package: ARRm normalization for Illumina methylation data
getBackground: Estimate background intensity from the negative control...
getCoefficients: Return the coefficients from the ARRm linear model
getDesignInfo: Build the chip and position indices
getQuantiles: Return the percentiles of a betaMatrix for each probe type
normalizeARRm: Perform ARRm normalization
positionPlots: Plots to evalue chip position effects on different...
ProbesType: Probe Design information for the 450k methylation assay
quantilePlots: Diagnostic plots for evaluation of background effects and dye...

Functions

ARRm.regression Man page Source code
ARRmNormalization Man page
ARRmNormalization-package Man page
ProbesType Man page
getBackground Man page Source code
getCoefficients Man page Source code
getDesignInfo Man page Source code
getQuantiles Man page Source code
normalizeARRm Man page Source code
normalizeI Man page Source code
normalizeII Man page Source code
positionPlots Man page Source code
quantilePlots Man page Source code

Files

DESCRIPTION
NAMESPACE
R
R/NormalizeARRm.R
build
build/vignette.rds
data
data/ProbesType.rda
inst
inst/doc
inst/doc/ARRmNormalization.R
inst/doc/ARRmNormalization.Rnw
inst/doc/ARRmNormalization.pdf
man
man/ARRmNormalization-internal.Rd
man/ARRmNormalization-package.Rd
man/ProbesType.Rd
man/getBackground.Rd
man/getCoefficients.Rd
man/getDesignInfo.Rd
man/getQuantiles.Rd
man/normalizeARRm.Rd
man/positionPlots.Rd
man/quantilePlots.Rd
vignettes
vignettes/ARRmNormalization.Rnw
ARRmNormalization documentation built on May 20, 2017, 9:59 p.m.

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