PIM: Given bisulfite sequencing data, calculates the proportion of...

In databio/RPIM: Assess epigenetic heterogeneity with proportion of intermediate methylation

Description

Given bisulfite sequencing data, calculates the proportion of intermediate methylation sites.

Usage

PIM(bsData, cacheDir = getOption("RESOURCES.RCACHE"), imLower = 0.25,
  imUpper = 0.75, confLevel = 0.95)

Arguments

bsData	Bisulfite sequencing data;
cacheDir	If using caching, this argument specifies the directory to use for storing the cache; defaults to global option for RESOURCES.RACHE; if no such option has been specified you must provide one
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

Value

A single value (numeric vector of length 1) indicating the proportion of intermediate methylation (PIM) of an individual sample

Examples

data("exampleBSDT", package="epihet")

if (require(simpleCache)) {
PIM(exampleBSDT, cacheDir="~")

simpleCache::setSharedCacheDir("cache")
PIM(exampleBSDT)
PIM(exampleBSDT, cacheDir="~", imLower=.2, imUpper=.8)
}

databio/RPIM documentation built on May 14, 2019, 2:41 p.m.