methylumi-package

methylumi

This package contains a class structure for handling methylation data
from Illumina as well as utility functions for loading the data from
files generated by Illumina. Normalization that attempts to correct for
dye bias is also included.Important data classes include: <code><links4class>MethyLumiSet</links4class></code> and
<code><links4class>MethyLumiQC</links4class></code>, both of which are subsets of the
<code><links4class>MethyLumi</links4class></code> class, which is a subset of the
<code><links4class>eSet</links4class></code> class.A worked example of the use of the package can be found by typing:
<code>openVignette()</code>.A full listing of the available documentation can be obtained by typing
<code>help.start()</code> and selecting <code>methylumi</code> from the <code>Packages</code>
link or by typing <code>library(help="methylumi")</code>.If you use the methylumIDAT function or its out-of-band preprocessing mechanisms in your work, a citation to the paper "Low-level processing of Illumina Infinium DNA methylation beadarrays" by TJ Triche, DJ Weisenberger, D Van Den Berg, KD Siegmund, and PW Laird, Nucleic acids research, 2013, would be appreciated.

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.

Sean Davis

Handle Illumina methylation data

methylumi-package function

This package contains a class structure for handling methylation data
from Illumina as well as utility functions for loading the data from
files generated by Illumina. Normalization that attempts to correct for
dye bias is also included.

Important data classes include: <code><linkS4class>MethyLumiSet</linkS4class></code> and
<code><linkS4class>MethyLumiQC</linkS4class></code>, both of which are subsets of the
<code><linkS4class>MethyLumi</linkS4class></code> class, which is a subset of the
<code><linkS4class>eSet</linkS4class></code> class.

A worked example of the use of the package can be found by typing:
<code>openVignette()</code>.

A full listing of the available documentation can be obtained by typing
<code>help.start()</code> and selecting <code>methylumi</code> from the <code>Packages</code>
link or by typing <code>library(help="methylumi")</code>.

If you use the methylumIDAT function or its out-of-band preprocessing mechanisms in your work, a citation to the paper "Low-level processing of Illumina Infinium DNA methylation beadarrays" by TJ Triche, DJ Weisenberger, D Van Den Berg, KD Siegmund, and PW Laird, Nucleic acids research, 2013, would be appreciated.

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methylumi-package: Handle Illumina methylation data

Description

Arguments

Details

References

See Also