methPercent {charm} | R Documentation |
Estimate percentage DNA methylation from log-ratios
methPercent(m, pmIndex, ngc, commonParams = TRUE)
m |
a matrix of M-values (methylation log-ratios). One column per sample. |
pmIndex |
A vector of probe indices to use in the calculation. Usually set to the indices of the pm probes (excluding background and other non-specific controls) by using pmIndex=pmindex(dat) |
ngc |
a vector with GC-content of probes. Same length as nrow(m) |
commonParams |
boolean indicating whether a common set of parameters should be used for all samples when converting M-values to percentage methylation. |
This function estimates percentage DNA methylation from normalized methylation log-ratios (M-values).
a matrix of percentage methylation estimates. Same dimensions as m
Martin Aryee <aryee@jhu.edu>
if (require(charmData) & require(BSgenome.Hsapiens.UCSC.hg18)) { phenodataDir <- system.file("extdata", package="charmData") pd <- read.delim(file.path(phenodataDir, "phenodata.txt")) pd <- subset(pd, sampleID=="441_liver") dataDir <- system.file("data", package="charmData") setwd(dataDir) # Read in raw data rawData <- readCharm(files=pd$filename, sampleKey=pd) # Find non-CpG control probes ctrlIdx <- getControlIndex(rawData, subject=Hsapiens) # Get normalized methylation log-ratios m <- methp(rawData, controlIndex=ctrlIdx, returnM=TRUE) # Estimate percentage methylation ngc <- countGC(rawData) p <- methPercent(m, ngc=ngc) }