reldist: Calculate the relative distance between two sets of intervals

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

Description

Calculate the relative distance between two sets of intervals

Usage

reldist(
	x,
	y,
	detail = FALSE,
	check.zero.based = TRUE,
	check.chr = TRUE,
	check.valid = TRUE,
	check.sort =TRUE,
	check.merge = TRUE,
	verbose = TRUE
	)

Arguments

x	firt region to be compared
y	second region to be compared
detail	should the relative distance be printed for every region
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	should regions be checked for sort order
check.merge	should overlapping regions be checked
verbose	should log messages and checking take place

Details

The frequency of relative distances in bins spanning 0 to 0.5

Author(s)

Daryl Waggott

References

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

See Also

jaccard

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 = "");
reldist(a,b);

}

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.