Handle Illumina methylation data

Documentation for package ‘methylumi’ version 1.6.1

DESCRIPTION file.
Overview of user guides and package vignettes; browse directory.

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methylumi-package	Handle Illumina methylation data
betas	methylumi accessors
betas-method	Class to hold Illumina Methylation data
betas<-	methylumi accessors
betas<--method	Class to hold Illumina Methylation data
boxplot-method	Class to hold Illumina Methylation data
combine-method	Class to hold Illumina Methylation data
controlTypes	Methods for dealing with control data for Illumina methylation data.
controlTypes-method	Class to hold Illumina Methylation QC data
controlTypes-method	Class to hold Illumina Methylation data
corplot	methylumi accessors
corplot-method	Class to hold Illumina Methylation data
exprs-method	Class to hold Illumina Methylation QC data
exprs-method	Class to hold Illumina Methylation data
exprs<--method	Class to hold Illumina Methylation QC data
exprs<--method	Class to hold Illumina Methylation data
extractBarcodeAndPosition	Extract the Barcode and Position Information from Sentrix ID
getAssayDataNameSubstitutions	Return a data.frame of AssayData name substitutions.
getHistory	methylumi accessors
getHistory-method	Class to hold Illumina Methylation data
hist-method	Class to hold Illumina Methylation data
initialize-method	Class to hold Illumina Methylation QC data
initialize-method	Class to hold Illumina Methylation data
methylated	methylumi accessors
methylated-method	The base class for storing Illumina Methylation data
methylated-method	Class to hold Illumina Methylation data
methylated<-	methylumi accessors
methylated<--method	The base class for storing Illumina Methylation data
methylated<--method	Class to hold Illumina Methylation data
methylumi	Handle Illumina methylation data
MethyLumi-class	The base class for storing Illumina Methylation data
MethyLumiQC-class	Class to hold Illumina Methylation QC data
methylumiR	Load data from Illumina methylation platform
MethyLumiSet-class	Class to hold Illumina Methylation data
mldat	Example SAM format Illumina methylation dataset
normalizeMethyLumiSet	Normalize a MethyLumiSet, accounting for dye bias
pairs-method	Class to hold Illumina Methylation data
plotSampleIntensities	Plot the sample intensities.
plotSampleIntensities-method	Class to hold Illumina Methylation data
pvals	methylumi accessors
pvals-method	The base class for storing Illumina Methylation data
pvals<-	methylumi accessors
pvals<--method	The base class for storing Illumina Methylation data
QCdata	methylumi accessors
QCdata-method	Class to hold Illumina Methylation data
QCdata<-	methylumi accessors
QCdata<--method	Class to hold Illumina Methylation data
QCDataOrNULL-class	Class to hold Illumina Methylation QC data
qcplot	Methods for dealing with control data for Illumina methylation data.
qcplot-method	The base class for storing Illumina Methylation data
qcplot-method	Class to hold Illumina Methylation QC data
qcplot-method	Class to hold Illumina Methylation data
show-method	Class to hold Illumina Methylation data
summary-method	The base class for storing Illumina Methylation data
unmethylated	methylumi accessors
unmethylated-method	The base class for storing Illumina Methylation data
unmethylated-method	Class to hold Illumina Methylation data
unmethylated<-	methylumi accessors
unmethylated<--method	The base class for storing Illumina Methylation data
unmethylated<--method	Class to hold Illumina Methylation data
[-method	Class to hold Illumina Methylation data