MassArray (version 1.24.0)

analyzeCpGs: Analyze CG methylation

Description

Function to determine percent methylation for all CGs from input fragmentation

Usage

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

Arguments

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")

Value

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

Details

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

See Also

See Also calcMeth

Examples

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)")