MassArray: Analytical Tools for MassArray Data
Version 1.28.0

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.

Browse man pages Browse package API and functions Browse package files

AuthorReid F. Thompson <rthompso@aecom.yu.edu>, John M. Greally <jgreally@aecom.yu.edu>
Bioconductor views DNAMethylation DataImport Genetics MassSpectrometry SNP Visualization
Date of publicationNone
MaintainerReid F. Thompson <rthompso@aecom.yu.edu>
LicenseGPL (>=2)
Version1.28.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("MassArray")

Man pages

ampliconPrediction: Amplicon prediction
analyzeCpGs: Analyze CG methylation
bisConvert: Bisulphite conversion
calcMeth: Calculate percent methylation
calcMW: Calculate molecular weight
calcPercentAdduct: Calculate percent salt adducts
calcPercentConversion: Calculate percent conversion
combine: Combine MassArrayData objects
combine-methods: Combine MassArrayData objects (methods)
convControl: Conversion control
countCGs: Count number of CGs
createWiggle: Create wiggle track
estimatePrimerDimer: Estimate Primer Dimers
evaluateSNPs: Evaluate SNPs
expandSequence: Expand nucleotide sequence
findCollisions: Find peak collisions
findFragments: Find fragments
findPeaks: Find peaks
identifySNPs: Identify SNPs
importEpiTyperData: Import EpiTyper data (v.1.0)
importEpiTyperData.new: Import EpiTyper data (v.1.0.5)
inSilicoFragmentation: In silico fragmentation
isAssayable: Is assayable?
MassArrayData-class: Class "MassArrayData"
MassArray.example.data: MassArray Data object
MassArrayFragment-class: Class "MassArrayFragment"
MassArrayPeak-class: Class "MassArrayPeak"
MassArraySpectrum-class: Class "MassArraySpectrum"
numCollisions: Count peak collisions
plot.MassArrayData: Plot MassArrayData
position: Operate on positional information
position-methods: Operate on positional information (methods)
revComplement: Reverse complement
revComplement-methods: Reverse complement (methods)
rnaDigest: RNA digest
samples: Operate on sample name(s)
samples-methods: Operate on sample name(s) (methods)
sum.MassArraySpectrum: Sum MassArraySpectrum objects

Functions

$,MassArrayData-method Man page
$,MassArrayFragment-method Man page
$,MassArrayPeak-method Man page
$,MassArraySpectrum-method Man page
$<-,MassArrayData-method Man page
$<-,MassArrayFragment-method Man page
$<-,MassArrayPeak-method Man page
$<-,MassArraySpectrum-method Man page
MassArray.example.data Man page
MassArrayData-class Man page
MassArrayFragment-class Man page
MassArrayPeak-class Man page
MassArraySpectrum-class Man page
[,MassArrayData-method Man page
ampliconPrediction Man page Source code
analyzeCpGs Man page Source code
bisConvert Man page Source code
calcMW Man page Source code
calcMeth Man page Source code
calcPercentAdduct Man page Source code
calcPercentConversion Man page Source code
combine Man page
combine,MassArrayData,MassArrayData-method Man page
combine,MassArrayData,missing-method Man page
combine-methods Man page
convControl Man page Source code
countCGs Man page Source code
createWiggle Man page Source code
estimatePrimerDimer Man page Source code
evaluateSNPs Man page Source code
expandSequence Man page Source code
findCollisions Man page Source code
findFragments Man page Source code
findPeaks Man page Source code
identifySNPs Man page Source code
importEpiTyperData Man page Source code
importEpiTyperData.new Man page Source code
inSilicoFragmentation Man page Source code
initialize,MassArrayData-method Man page
initialize,MassArrayFragment-method Man page
initialize,MassArrayPeak-method Man page
initialize,MassArraySpectrum-method Man page
isAssayable Man page Source code
numCollisions Man page Source code
plot.MassArrayData Man page Source code Source code
position Man page
position,MassArrayData-method Man page
position-methods Man page
position<- Man page
position<-,MassArrayData,character-method Man page
position<-,MassArrayData,missing-method Man page
revComplement Man page
revComplement,MassArrayData-method Man page
revComplement,character-method Man page
revComplement-methods Man page
rnaDigest Man page Source code
samples Man page
samples,MassArrayData-method Man page
samples-methods Man page
samples<- Man page
samples<-,MassArrayData,character-method Man page
samples<-,MassArrayData,missing-method Man page
sum.MassArraySpectrum Man page Source code Source code

Files

DESCRIPTION
NAMESPACE
R
R/MassArrayData.R
R/MassArrayFragment.R
R/MassArrayPeak.R
R/MassArraySpectrum.R
R/ampliconPrediction.R
R/bisConvert.R
R/calcMW.R
R/calcPercentConversion.R
R/combine.R
R/convControl.R
R/countCGs.R
R/createWiggle.R
R/estimatePrimerDimer.R
R/evaluateSNPs.R
R/findCollisions.R
R/identifySNPs.R
R/importEpiTyperData.R
R/inSilicoFragmentation.R
R/isAssayable.R
R/plot.MassArrayData.R
R/position.R
R/revComplement.R
R/rnaDigest.R
R/samples.R
R/sum.MassArraySpectrum.R
build
build/vignette.rds
data
data/MassArray.example.data.RData
inst
inst/doc
inst/doc/MassArray.R
inst/doc/MassArray.Rnw
inst/doc/MassArray.pdf
inst/extdata
inst/extdata/Example.txt
man
man/MassArray.example.data.Rd
man/MassArrayData-class.Rd
man/MassArrayFragment-class.Rd
man/MassArrayPeak-class.Rd
man/MassArraySpectrum-class.Rd
man/ampliconPrediction.Rd
man/analyzeCpGs.Rd
man/bisConvert.Rd
man/calcMW.Rd
man/calcMeth.Rd
man/calcPercentAdduct.Rd
man/calcPercentConversion.Rd
man/combine-methods.Rd
man/combine.Rd
man/convControl.Rd
man/countCGs.Rd
man/createWiggle.Rd
man/estimatePrimerDimer.Rd
man/evaluateSNPs.Rd
man/expandSequence.Rd
man/findCollisions.Rd
man/findFragments.Rd
man/findPeaks.Rd
man/identifySNPs.Rd
man/importEpiTyperData.Rd
man/importEpiTyperData.new.Rd
man/inSilicoFragmentation.Rd
man/isAssayable.Rd
man/numCollisions.Rd
man/plot.MassArrayData.Rd
man/position-methods.Rd
man/position.Rd
man/revComplement-methods.Rd
man/revComplement.Rd
man/rnaDigest.Rd
man/samples-methods.Rd
man/samples.Rd
man/sum.MassArraySpectrum.Rd
vignettes
vignettes/MassArray.Rnw
vignettes/MassArray.bib
vignettes/conversion.pdf
MassArray documentation built on May 20, 2017, 9:59 p.m.