get.random.regions: generates a set of random regions

In bedr: Genomic Region Processing using Tools Such as 'BEDTools', 'BEDOPS' and 'Tabix'

Description

generates a set of random regions for a specific species/build. Choices are human (hg18, hg19), mouse(mm9, mm10). regions are sampled from a log-normal distribution.

Usage

get.random.regions(
	n = 10,
	chr = NULL,
	species = "human",
	build = "hg19",
	size.mean = 10,
	size.sd = 0.25,
	mask.gaps = FALSE,
	mask.repeats = FALSE,
	sort.output = TRUE,
	verbose = TRUE
	)

Arguments

n	number of regions
chr	the chr or region
species	species
build	build
size.mean	region mean in log space
size.sd	region sd in log space
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.
sort.output	return a sorted index
verbose	words

Author(s)

Daryl Waggott

Examples

test.regions <- get.random.regions(100)

Example output

######################
#### bedr v1.0.7 ####
######################

checking binary availability...
  * Checking path for bedtools... FAIL
  * Checking path for bedops... FAIL
  * Checking path for tabix... FAIL
tests and examples will be skipped on R CMD check if binaries are missing

bedr documentation built on May 2, 2019, 11:36 a.m.