R/missMethyl-package.R

In Oshlack/missMethyl: Analysing Illumina HumanMethylation BeadChip Data

#' Introduction to the missMethyl package
#' 
#' missMethyl is a library for the analysis of Illumina's 450K human
#' methylation BeadChip. Specifically, functions for SWAN normalisation and
#' differential variability analysis are provided. SWAN normalisation uses
#' probe specific information, and the differential variability procedure uses
#' linear models which can handle any designed experiment.
#' 
#' \tabular{ll}{ Package: \tab missMethyl\cr Type: \tab Package\cr Version:
#' \tab 0.99.0\cr Date: \tab 2014-06-30\cr License: \tab GPL-2\cr }
#' Normalisation of the 450K arrays can be performed using the function
#' \code{SWAN}.
#' 
#' Differential variability analysis can be performed by calling \code{varFit}
#' followed by \code{topVar} for a list of the top ranked differentially
#' variable CpGs between conditions.
#' 
#' More detailed help documentation is provided in each function's help page.
#' 
#' @name missMethyl-package
#' @aliases missMethyl-package missMethyl
#' @docType package
#' @author Belinda Phipson and Jovana Maksimovic
#' 
#' Maintainer: Belinda Phipson <belinda.phipson@@mcri.edu.au>, Jovana
#' Maksimovic <jovana.maksimovic@@petermac.org>
#' @references Maksimovic, J., Gordon, L., Oshlack, A. (2012).  SWAN:
#' Subset-quantile within array normalization for illumina infinium
#' HumanMethylation450 BeadChips. \emph{Genome Biology}, 13:R44.
#' 
#' Phipson, B., and Oshlack, A. (2014). DiffVar: A new method for detecting
#' differential variability with application to methylation in cancer and
#' aging. \emph{Genome Biology}, \bold{15}:465.
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