analyzeCpGs: Analyze CG methylation
In MassArray: Analytical Tools for MassArray Data

Description Usage Arguments Details Value Author(s) See Also Examples

Function to determine percent methylation for all CGs from input fragmentation

1	analyzeCpGs(fragments, peaks, method = c("weighted", "proportion"))

`fragments`	List of MassArrayFragment objects
`peaks`	List of MassArrayPeak objects comprising spectral data for a given assay
`method`	Specifies which algorithm to use when calculating percent methylation (either "weighted" or "proportion")

Wrapper function for calcMeth(), takes fragmentation pattern and spectral data as input and applies percent methylation calculation for all CG-containing, non conversion control fragments

Returns a list of numerical values corresponding to percent methylation for each CG dinucleotide, with 0

Reid F. Thompson (rthompso@aecom.yu.edu), John M. Greally (jgreally@aecom.yu.edu)

See Also calcMeth

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data(MassArray.example.data)
cpg.data <- analyzeCpGs(MassArray.example.data$fragments.T, MassArray.example.data$samples[[1]]$peaks, method="weighted")
barplot(cpg.data, xlab="CpG (Number)", ylim=c(0,1), ylab="Methylation (Percent)")