MassArray: Analytical Tools for MassArray Data

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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@aecom.yu.edu>, John M. Greally <jgreally@aecom.yu.edu>
Date of publication
None
Maintainer
Reid F. Thompson <rthompso@aecom.yu.edu>
License
GPL (>=2)
Version
1.26.0

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

Files in this package

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