MassArray: Analytical Tools for MassArray Data

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.

AuthorReid F. Thompson <rthompso@aecom.yu.edu>, John M. Greally <jgreally@aecom.yu.edu>
Date of publicationNone
MaintainerReid F. Thompson <rthompso@aecom.yu.edu>
LicenseGPL (>=2)
Version1.26.0

View on Bioconductor

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

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

Files

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

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