MassArray

Analytical Tools for MassArray Data

Bioconductor version: Release (2.7)

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, John M. Greally

Maintainer: Reid F. Thompson

To install this package, start R and enter:

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

Documentation

PDF	R Script	1. Primer
PDF		conversion.pdf

Reference Manual

Details

biocViews	DNAMethylation, SNP, MassSpectrometry, Genetics, DataImport, Visualization
Depends	R, methods
Imports	graphics, grDevices, methods, stats, utils
Suggests
System Requirements
License	GPL (>=2)
URL
Depends On Me
Imports Me
Suggests Me
Version	1.2.0

Package Downloads

Package Source	MassArray_1.2.0.tar.gz
Windows Binary	MassArray_1.2.0.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary	MassArray_1.2.0.tgz
Package Downloads Report	Download Stats