RPIM: Calculate the relative proportion of intermediate methylation...

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

Description

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.

Usage

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

Arguments

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 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 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

References

http://github.com/databio/epihet

Examples

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

if (require(simpleCache)) {
RPIM(BSDTlist, cacheDir="~")

simpleCache::setSharedCacheDir("cache")
RPIM(BSDTlist)
RPIM(BSDTlist, imLower=.2, imUpper=.8)
}

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