Description Usage Arguments Value Examples
Given bisulfite sequencing data, calculates the proportion of intermediate methylation sites.
1 2 
bsData 
Bisulfite sequencing data; 
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 single value (numeric vector of length 1) indicating the proportion of intermediate methylation (PIM) of an individual sample
1 2 3 4 5 6 7 8 9  data("exampleBSDT", package="epihet")
if (require(simpleCache)) {
PIM(exampleBSDT, cacheDir="~")
simpleCache::setSharedCacheDir("cache")
PIM(exampleBSDT)
PIM(exampleBSDT, cacheDir="~", imLower=.2, imUpper=.8)
}

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