Get Region Methylation Data

getRegionMeth() extracts methylation values at specified regions for all samples and then saves it as a .rds file.

Usage

getRegionMeth(
  regions,
  bs,
  type = c("raw", "smooth"),
  save = TRUE,
  file = "Region_Methylation.rds",
  verbose = TRUE
)

Arguments

regions

A data.frame of regions, typically after filtering with filterRegions(). Must have the columns chr, start, and end.

bs

A BSseq object, typically after filtering with filterCpGs().

type

A character(1) specifying the type of methylation values to extract. Accepted values are raw and smooth

save

A logical(1) indicating whether to save the matrix.

file

A character(1) giving the file name (.rds) for the saved matrix.

verbose

A logical(1) indicating whether messages should be printed.

Value

A numeric matrix, where each row is a region and each column is a sample.

Details

Methylation is summarized at the region level, and is estimated as the methylated reads divided by the total reads. Methylation values are obtained from a BSseq object and can be either raw or smoothed methylation.

See also

• getPCs() and adjustRegionMeth() to adjust methylation for the top principal components.

• getDendro() and plotDendro() to generate and visualize dendrograms.

Examples

if (FALSE) {

# Get Methylation Data
meth <- getRegionMeth(regions, bs = bs, file = "Region_Methylation.rds")

# Adjust Methylation Data for Top PCs
mod <- model.matrix(~1, data = pData(bs))
PCs <- getPCs(meth, mod = mod, file = "Top_Principal_Components.rds")
methAdj <- adjustRegionMeth(meth, PCs = PCs,
                            file = "Adjusted_Region_Methylation.rds")

# Assess Sample Similarity
getDendro(methAdj, distance = "euclidean") %>%
        plotDendro(file = "Sample_Dendrogram.pdf", expandY = c(0.25,0.08))
}