bedr.merge.region: merge i.e. collapse overlpaping regions

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

Description

merge i.e. collapse overlpaping regions

Usage

bedr.merge.region(
	x,
	distance = 0,
	list.names = TRUE,
	number = FALSE,
	stratify.by = NULL,
	check.zero.based = TRUE,
	check.chr = TRUE,
	check.valid = TRUE,
	check.sort = TRUE,
	verbose = TRUE
	);

Arguments

x	input
distance	maximum distance between regions to be merged. defaults to 0 which means overlapping or bookended features. note that you can use negative distances to enforce a minimum overlap.
list.names	output list of names for merged items
number	output number of merged items
stratify.by	a column name indicating the groups to stratify merging within i.e. gene name. merging will not happen between groups.
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 the sort order be checked
verbose	should log messages and checking take place

Author(s)

Daryl Waggott

References

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

Examples

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

index <- get.example.regions();

a <- index[[1]];

a.sort   <- bedr.sort.region(a);
a.merged <- bedr.merge.region(a.sort);

}

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.