Epihet calculates a the PIM score, which measures the epigenetic heterogeneity in a bisulfite sequencing sample. Under the assumption that a homogeneous sample will have mostly CpGs with either 100% or 0% DNA methylation, it follows that the proportion of sites that differ from these two extremes can be used as a measure of sample heterogeneity.
Install the development version of epihet directly from GitHub:
devtools::install_github("databio/epihet")
or locally after downloading/cloning the source code:
install.packages("path/to/epihet/directory", repos=NULL, type="source")
Please see the vignettes for details.