MassArray

Analytical Tools for MassArray Data

Bioconductor version: Development (3.0)

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.

Author: Reid F. Thompson <rthompso at aecom.yu.edu>, John M. Greally <jgreally at aecom.yu.edu>

Maintainer: Reid F. Thompson <rthompso at aecom.yu.edu>

To install this package, start R and enter:

    source("http://bioconductor.org/biocLite.R")
    biocLite("MassArray")

To cite this package in a publication, start R and enter:

    citation("MassArray")

Documentation

PDF R Script 1. Primer
PDF   Reference Manual

Details

biocViews DNAMethylation, DataImport, Genetics, MassSpectrometry, SNP, Software, Visualization
Version 1.17.0
In Bioconductor since BioC 2.6 (R-2.11)
License GPL (>=2)
Depends R (>= 2.10.0), methods
Imports graphics, grDevices, methods, stats, utils
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Package Downloads

Package Source MassArray_1.17.0.tar.gz
Windows Binary MassArray_1.17.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) MassArray_1.17.0.tgz
Mac OS X 10.9 (Mavericks)
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