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MassArray (version 1.24.0)

Analytical Tools for MassArray Data

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.

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Version

Version

1.24.0

License

GPL (>=2)

Maintainer

Reid F Thompson

Last Published

February 15th, 2017

Functions in MassArray (1.24.0)

expandSequence

Expand nucleotide sequence
ampliconPrediction

Amplicon prediction
calcPercentAdduct

Calculate percent salt adducts
position

Operate on positional information
findPeaks

Find peaks
rnaDigest

RNA digest
importEpiTyperData.new

Import EpiTyper data (v.1.0.5)
MassArrayFragment-class

Class "MassArrayFragment"
position-methods

Operate on positional information (methods)
calcMW

Calculate molecular weight
findCollisions

Find peak collisions
samples

Operate on sample name(s)
identifySNPs

Identify SNPs
numCollisions

Count peak collisions
MassArray.example.data

MassArray Data object
calcPercentConversion

Calculate percent conversion
evaluateSNPs

Evaluate SNPs
sum.MassArraySpectrum

Sum MassArraySpectrum objects
analyzeCpGs

Analyze CG methylation
estimatePrimerDimer

Estimate Primer Dimers
MassArrayPeak-class

Class "MassArrayPeak"
MassArrayData-class

Class "MassArrayData"
inSilicoFragmentation

In silico fragmentation
samples-methods

Operate on sample name(s) (methods)
convControl

Conversion control
revComplement-methods

Reverse complement (methods)
combine

Combine MassArrayData objects
importEpiTyperData

Import EpiTyper data (v.1.0)
countCGs

Count number of CGs
MassArraySpectrum-class

Class "MassArraySpectrum"
findFragments

Find fragments
isAssayable

Is assayable?
calcMeth

Calculate percent methylation
plot.MassArrayData

Plot MassArrayData
createWiggle

Create wiggle track
combine-methods

Combine MassArrayData objects (methods)
bisConvert

Bisulphite conversion
revComplement

Reverse complement