ARRmNormalization: Adaptive Robust Regression normalization for Illumina methylation data

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

Author
Jean-Philippe Fortin, Celia M.T. Greenwood, Aurelie Labbe.
Date of publication
None
Maintainer
Jean-Philippe Fortin <jfortin@jhsph.edu>
License
Artistic-2.0
Version
1.14.0

View on Bioconductor

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...

Files in this package

ARRmNormalization/DESCRIPTION
ARRmNormalization/NAMESPACE
ARRmNormalization/R
ARRmNormalization/R/NormalizeARRm.R
ARRmNormalization/build
ARRmNormalization/build/vignette.rds
ARRmNormalization/data
ARRmNormalization/data/ProbesType.rda
ARRmNormalization/inst
ARRmNormalization/inst/doc
ARRmNormalization/inst/doc/ARRmNormalization.R
ARRmNormalization/inst/doc/ARRmNormalization.Rnw
ARRmNormalization/inst/doc/ARRmNormalization.pdf
ARRmNormalization/man
ARRmNormalization/man/ARRmNormalization-internal.Rd
ARRmNormalization/man/ARRmNormalization-package.Rd
ARRmNormalization/man/ProbesType.Rd
ARRmNormalization/man/getBackground.Rd
ARRmNormalization/man/getCoefficients.Rd
ARRmNormalization/man/getDesignInfo.Rd
ARRmNormalization/man/getQuantiles.Rd
ARRmNormalization/man/normalizeARRm.Rd
ARRmNormalization/man/positionPlots.Rd
ARRmNormalization/man/quantilePlots.Rd
ARRmNormalization/vignettes
ARRmNormalization/vignettes/ARRmNormalization.Rnw