bedr.join.region: join two region objects using a left outer join

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

Description

join two region objects using a left outer join

Usage

bedr.join.region(
	x,
	y,
	fraction.overlap = 1/1e9,
	reciporical = FALSE,
	report.n.overlap = FALSE,
	check.zero.based = TRUE,
	check.chr = TRUE,
	check.valid = TRUE,
	check.sort = TRUE,
	check.merge = TRUE,
	verbose = TRUE
	)

Arguments

x	object a
y	object b
fraction.overlap	proportion of overlap to be considered a match
report.n.overlap	should the number of overlapping bases be reported
reciporical	should the fraction overlap be applied to object b as well
check.zero.based	should 0 based coordinates be checked
check.chr	should chr prefix be checked
check.valid	check if region is valid
check.sort	check if region is sorted
check.merge	check if overlapping regions are merged
verbose	messages and checks

Author(s)

Daryl Waggott

References

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

Examples

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

index <- get.example.regions();

a <- index[[1]];
b <- index[[2]];

a.sort <- bedr.sort.region(a);
b.sort <- bedr.sort.region(b);

d <- bedr.join.region(a.sort, b.sort);
}

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

  * Checking path for bedtools... FAIL

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