MassArraySpectrum-class

$,MassArraySpectrum-method

$<-,MassArraySpectrum-method

initialize,MassArraySpectrum-method

A data structure containing MassArray spectral data for a single sample

classes

This package is designed for the import, quality control, analysis, and visualization of methylation data generated using Sequenom's MassArray platform.  The tools herein contain a highly detailed amplicon prediction for optimal assay design.  Also included are quality control measures of data, such as primer dimer and bisulfite conversion efficiency estimation.  Methylation data are calculated using the same algorithms contained in the EpiTyper software package.  Additionally, automatic SNP-detection can be used to flag potentially confounded data from specific CG sites.  Visualization includes barplots of methylation data as well as UCSC Genome Browser-compatible BED tracks.  Multiple assays can be positionally combined for integrated analysis.

Reid F Thompson

MassArray

Analytical Tools for MassArray Data

MassArraySpectrum-class function

Objects can be created by calls of the form <code>new("MassArraySpectrum", sample, rxn, strand, peaks, quality.conversion, quality.spectra, quality.primerdimer, quality.contaminant, quality.adducts, ...)</code>.

Objects from the Class

<dl>
    <dt><code>sample</code>:</dt><dd>Sample name</dd> <dt><code>rxn</code>:</dt><dd>Cleavage reaction (either 'T' or 'C')</dd> <dt><code>strand</code>:</dt><dd>DNA strand for amplicon (either '+' or '-')</dd> <dt><code>peaks</code>:</dt><dd>List containing objects of class <code>MassArrayPeak</code></dd> <dt><code>quality.conversion</code>:</dt><dd>Overall level(s) of remnant unconverted cytosines, as measured by one or more conversion controls</dd> <dt><code>quality.spectra</code>:</dt><dd>(currently not supported)</dd> <dt><code>quality.primerdimer</code>:</dt><dd>(currently not supported)</dd> <dt><code>quality.contaminant</code>:</dt><dd>(currently not supported)</dd> <dt><code>quality.adducts</code>:</dt><dd>Overall ratio(s) of Na and/or K adduct peak heights to expected peak heights</dd> </dl> 

Slots

<dl>
    <dt>\$</dt><dd><code>signature(x = "MassArraySpectrum")</code>: ... </dd> <dt>\$&lt;-</dt><dd><code>signature(x = "MassArraySpectrum")</code>: ... </dd> <dt>initialize</dt><dd><code>signature(.Object = "MassArraySpectrum")</code>: ... </dd> </dl> 

MassArraySpectrum-class: Class "MassArraySpectrum"

Description

Arguments

Objects from the Class

Slots

Methods

See Also

Examples