Description Usage Arguments Value References Examples
Calculate the relative proportion of intermediate methylation (RPIM) score.
Provides a score called PIM that measures the epigenetic heterogeneity in a bisulfite sequencing sample. Under the assumption that a homogeneous sample will have mostly CpGs with either 100 follows that the proportion of sites that differ from these two extremes can be used as a measure of sample heterogeneity.
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bsData 
Bisulfite sequencing data for multiple samples. A list of BSDT (bisulfite data.table), one corresponds to each sample to test. This may also be a BSseq object 
cacheDir 
If using caching, this argument specifies the directory to
use for storing the cache; defaults to global option for

imLower 
The lower boundary for intermediate methylation (IM); if a site is entirely below this threshold (or if any part of its binomial credibility interval overlaps this boundary) it is not considered IM; defaults to .25 
imUpper 
The upper boundary for intermediate methylation (IM); if a site is entirely above this threshold (or if any part of its binomial credibility interval overlaps this boundary) it is not considered IM; defaults to .75 
confLevel 
A decimal indicating the level of confidence to be used while creating cached the binomial bayes credibility interval; default is .95 for 95 percent confidence 
A named vector of the same length as the number of samples being analyzed; each element in the vector represents the the average proportion of intermediate methylation relative to the other samples; all samples are represented and elements named accordingly
http://github.com/databio/epihet
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