classify_domains.double: Determine the group(s) to which a domain belongs

In ChristopherBarrington/domainClassifyR: Classification of Hi-C interaction domains

Description

A threshold of significance is applied to the calculated p-values, and a domain classification attributed.

Usage

classify_domains.double(contacts, types, measures = c("P", "Q", "p", "Z"),
  thresholds, p.thresholds = c(0.0001, 0.00000001), z.quantiles = c(0.5,
  0.75), z.thresholds = NULL)

Arguments

contacts	The list of domains generated from get_Q_values()
types	The names of the elements to iterate over; these are produced by get.fend.samples() and are usually POTENTIAL (if get.fends was TRUE) and OBSERVED
measures	The names of the p-value elements in Z_STATISTICS to iterate over; these are produced by get_Z_statistics()
thresholds	A list of significance thresholds to apply
p.threshold	The threshold to set for all p-value measures
z.quantile	The quantile of Z scores above which are considered significant
z.threshold	A threshold to apply, overriding z.quantile and ignoring 'types'

Details

The thresholds list is a 2-level list, the first level indicates the null method used (eg 'OBSERVED') and the second level specifies the measure (eg 'Q' or 'Z').

Value

The contacts list, with additional information in the Z_STATISTICS

ChristopherBarrington/domainClassifyR documentation built on May 3, 2019, 5:22 p.m.