bedr.subtract.region: subtracts features or ranges in object b from object a

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

Description

subtracts features or ranges in object b from object a

Usage

bedr.subtract.region(
	x,
	y,
	fraction.overlap = 1/1e9,
	remove.whole.feature = TRUE,
	check.zero.based = TRUE,
	check.chr = TRUE,
	check.valid = TRUE,
	check.sort = TRUE,
	check.merge = TRUE,
	verbose = TRUE
	)

Arguments

x	item a
y	item b
fraction.overlap	what portion of A to be considered an overlap
remove.whole.feature	should whole feature be removed
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
check.sort	check if region is sorted
check.merge	check if overlapping regions are merged
verbose	messages and checks

Value

Regions exclusive to one object of regions.

Author(s)

Daryl Waggott

References

http://bedtools.readthedocs.org/en/latest/content/tools/subtract.html

Examples

if (check.binary("bedtools")) {
index <- get.example.regions();

a <- index[[1]];
b <- index[[2]];
a <- bedr(engine = "bedtools", input = list(i = a), method = "sort", params = "");
b <- bedr(engine = "bedtools", input = list(i = b), method = "sort", params = "");
d <- bedr.subtract.region(a,b);
}

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 v1.0.3 ####
######################

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.