permute.region: permute a set of regions

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

Description

permute a set of regions

Usage

permute.region(
	x,
	stratify.by.chr = FALSE,
	species = "human",
	build = "hg19",
	chr.names = paste0("chr",c(1:22,"X","Y","M")),
	mask.gaps = FALSE,
	gaps.file = NULL,
	mask.repeats = FALSE,
	repeats.file = NULL,
	sort.output = TRUE,
	is.checked = FALSE,
	check.zero.based = TRUE,
	check.chr = TRUE,
	check.valid = TRUE,
	verbose = TRUE
	)

Arguments

x	regions 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
chr.names	names of the chromosomes to use
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. It defaults to off
gaps.file	database file of gaps. Defaults to Homo sapiens Hg19 gap.txt.gz file available through UCSC
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
repeats.file	database file of repeats as supplied by UCSC containing RepMasker data e.g rmsk.txt.gz
sort.output	should the output be sorted
is.checked	Has the input data already be tested for validity. This is often done once before multiple permutations.
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

Details

1. Sampling with replacement on region length. 2. Sampling with replacement on start positions. Positions that contain Ns in the reference are set to 0 weight during sampling.

Regions that overlap the end of a chromosome or gap are trimmed.

Steps 1 and 2 are done within chromosomes if stratify.by.chr is set to true.

Value

A region object with randomized start positions.

Author(s)

Daryl Waggott

Examples

if (check.binary("bedtools")) {

index <- get.example.regions();
a <- index[[1]];
a <- bedr(engine = "bedtools", input = list(i = a), method = "sort", params = "");
a.perm <- permute.region(a);

}

Example output

sh: 1: cannot create /dev/null: Permission denied
sh: 1: cannot create /dev/null: Permission denied
sh: 1: cannot create /dev/null: Permission denied


######################
#### 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

  * Checking path for bedtools... sh: 1: cannot create /dev/null: Permission denied
FAIL

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