test.region.similarity: Compare sets of regions via jaccard and relative distance using permutation

Description

Compare sets of regions via jaccard and relative distance using permutation to get an empirical p-value.

Usage

test.region.similarity(
	x,
	y,
	n = 1000,
	stratify.by.chr = FALSE,
	species = "human",
	build = "hg19",
	mask.gaps = FALSE,
	mask.repeats = FALSE,
	gaps.file = NULL,
	repeats.file = NULL,
	check.zero.based = TRUE,
	check.chr = TRUE,
	check.valid = TRUE,
	verbose = TRUE
	)

Value

A list of results

Arguments

x: first region to be compared. this is the region that is permuted
y: second region to be compared
n: the number of iterations to permute
stratify.by.chr: Should the permutation be happen separetely for each chromosome. That is are chromosomes exchangeable.
species: species
build: the build of the reference
mask.gaps: should the gaps (Ns) in the human reference be ignored as potential start points. This drammatically increases memory and run time but is more appropriate in almost all settings. By default it's off.
mask.repeats: should the repeats from repeatMasker be ignored as potential start points. This drammatically increases memory and run time but is more appropriate in almost all settings. By default it's off.
gaps.file: database file of gaps. Defaults to Homo sapiens Hg19 gap.txt.gz file available through UCSC
repeats.file: database file of repeats as supplied by UCSC containing RepMasker data e.g rmsk.txt.gz
check.zero.based: should 0 based coordinates be checked
check.chr: should chr prefix be checked
check.valid: should the region be checkded for integerity
verbose: should log messages and checking take place

Author

Daryl Waggott

Details

Iteratively permutes intervals and recalculates jaccard and reldist statistics.