prepIM: Prepares the intermediate methylation (IM) table

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

Description

Prepares the intermediate methylation (IM) table

Usage

prepIM(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; default is .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; default is .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 data.table object with the following columns:

• chr chromosome of methylation read

• start starting position for methylation read

• IM boolean indicator of itermediate methylation status

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