This package provides classes for holding and manipulating Illumina methylation data. Based on eSet, it can contain MIAME information, sample information, feature information, and multiple matrices of data. An "intelligent" import function, methylumiR can read the Illumina text files and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from HumanMethylation27 and HumanMethylation450 microarrays. Normalization, background correction, and quality control features for GoldenGate, Infinium, and Infinium HD arrays are also included.
|Author||Sean Davis, Pan Du, Sven Bilke, Tim Triche, Jr., Moiz Bootwalla|
|Date of publication||None|
|Maintainer||Sean Davis <firstname.lastname@example.org>|
CpGs: Data frame describing loci on the 27 and 450k arrays.
estimateM: Estimate methylation M-value matrix
extractBarcodeAndPosition: Extract the Barcode and Position Information from Sentrix ID
featureFilter: Annotation-based Filtering of Features (CpG sites) in a...
generics: methylumi accessors
getAssayDataNameSubstitutions: Return a data.frame of AssayData name substitutions.
methylData-class: Class '"methylData"', superclass for MethyLumiSet and...
MethyLumi-class: The base class for storing Illumina Methylation data
methylumiGenerics: Generics defined in methylumi
MethyLumiM-class: Class "MethyLumiM": for Illumina Methylation microarray data...
methylumi-package: Handle Illumina methylation data
MethyLumiQC-class: Class '"MethyLumiQC"' for holding Illumina methylation QC...
methylumiR: Load data from Illumina methylation platform
MethyLumiSet-class: Class '"MethyLumiSet"' for containing Illumina methylation...
mldat: Example SAM format Illumina methylation dataset
normalizeMethyLumiSet: Normalize a MethyLumiSet, accounting for dye bias
plotSampleIntensities: Plot the sample intensities.
qcplot: Methods for dealing with control data for Illumina...
stripBeadExtras: Strip excessive probe-level data from MethyLumiSets
varFilter: Variation-based Filtering of Features (CpG sites) in a...