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methylumi (version 2.12.0)

Handle Illumina methylation data

Description

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.

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Version

Version

2.12.0

License

GPL-2

Maintainer

Sean Davis

Last Published

February 15th, 2017

Functions in methylumi (2.12.0)

getAssayDataNameSubstitutions

Return a data.frame of AssayData name substitutions.
MethyLumi-accessors

methylumi accessors
methylumi-package

Handle Illumina methylation data
extractBarcodeAndPosition

Extract the Barcode and Position Information from Sentrix ID
methylData-class

Class "methylData", superclass for MethyLumiSet and MethyLumiM
methylumIDAT

methylumIDAT
MethyLumi-class

The base class for storing Illumina Methylation data
featureFilter

Annotation-based Filtering of Features (CpG sites) in a MethyLumiSet or MethyLumiM object
estimateM

Estimate methylation M-value matrix
CpGs

Data frame describing loci on the 27 and 450k arrays.
qcplot

Methods for dealing with control data for Illumina methylation data.
mldat

Example SAM format Illumina methylation dataset
methylumiGenerics

Generics defined in methylumi
methylumiR

Load data from Illumina methylation platform
normalizeMethyLumiSet

Normalize a MethyLumiSet, accounting for dye bias
MethyLumiM-class

Class "MethyLumiM": for Illumina Methylation microarray data using logRatios
plotSampleIntensities

Plot the sample intensities.
MethyLumiQC-class

Class "MethyLumiQC" for holding Illumina methylation QC data
MethyLumiSet-class

Class "MethyLumiSet" for containing Illumina methylation data
MethyLumi-strippers

Strip excessive probe-level data from MethyLumiSets
varFilter

Variation-based Filtering of Features (CpG sites) in a MethyLumiSet or MethyLumiM object