bedr (version 1.0.7)

reldist: Calculate the relative distance between two sets of intervals

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

Author

Daryl Waggott

Details

The frequency of relative distances in bins spanning 0 to 0.5

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);

}