analyzeCpGs {MassArray} | R Documentation |
Function to determine percent methylation for all CGs from input fragmentation
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
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)")