MassArray

Package: MassArray
Type: Package
Title: Analytical Tools for MassArray Data
Version: 1.24.0
Date: 2009-05-19
Author: Reid F. Thompson <rthompso@aecom.yu.edu>, John M. Greally <jgreally@aecom.yu.edu>
Maintainer: Reid F. Thompson <rthompso@aecom.yu.edu>
Imports: graphics, grDevices, methods, stats, utils
Depends: R (>= 2.10.0), methods
Description: 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.
License: GPL (>=2)
biocViews: DNAMethylation, SNP, MassSpectrometry, Genetics, DataImport,
Visualization
LazyData: yes
LazyLoad: yes
NeedsCompilation: no
Packaged: 2016-05-04 03:27:09 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'MassArray' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'MassArray'
    finding HTML links ... done
    MassArray.example.data                  html  
    MassArrayData-class                     html  
    MassArrayFragment-class                 html  
    MassArrayPeak-class                     html  
    MassArraySpectrum-class                 html  
    ampliconPrediction                      html  
    analyzeCpGs                             html  
    bisConvert                              html  
    calcMW                                  html  
    calcMeth                                html  
    calcPercentAdduct                       html  
    calcPercentConversion                   html  
    combine-methods                         html  
    combine                                 html  
    convControl                             html  
    countCGs                                html  
    createWiggle                            html  
    estimatePrimerDimer                     html  
    evaluateSNPs                            html  
    expandSequence                          html  
    findCollisions                          html  
    findFragments                           html  
    findPeaks                               html  
    identifySNPs                            html  
    importEpiTyperData                      html  
    importEpiTyperData.new                  html  
    inSilicoFragmentation                   html  
    isAssayable                             html  
    numCollisions                           html  
    plot.MassArrayData                      html  
    position-methods                        html  
    position                                html  
    revComplement-methods                   html  
    revComplement                           html  
    rnaDigest                               html  
    samples-methods                         html  
    samples                                 html  
    sum.MassArraySpectrum                   html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (MassArray)
Making 'packages.html' ... done