calculateRPIM: Helper function to get the relative proportion of flagged...

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

Description

Helper function to get the relative proportion of flagged sites for a single sample versus all other samples

Usage

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

Arguments

sampleBaseline	The sample (which should specify a name in the bisulfite sequencing data) to use as the baseline the proportion of sites for.
sampleRelative	The sample to compare relatively to the baseline sample for the proportion of sites.
bsData	Bisulfite sequencing data for multiple samples; a BSDT (bisulfite data.table) that has been split with splitDataTable (so, a list of BSDTs); one corresponds to each sample to test.
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 vector of the same length as the number of samples being analyzed; each element in the vector represents the the proportion of intermediate methylation relative to the other samples for a single sample

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