bedr.join.multiple.region: join multiple region objects

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

Description

join multiple objects

Usage

bedr.join.multiple.region(
	x = list(),
	fraction.overlap = 1/1e9,
	empty = FALSE,
	missing.values = ".",
	cluster = FALSE,
	species = "human",
	build = "hg19",
	check.zero.based = TRUE,
	check.chr = TRUE,
	check.valid = TRUE,
	check.sort = TRUE,
	check.merge = TRUE,
	verbose = TRUE
	)

Arguments

x	list of region objects
fraction.overlap	proportion of bases to be considered an overlap
empty	print rows if no match
missing.values	missing value character
cluster	TRUE/FALSE for clustering
species	species i.e. human or mouse
build	genome build to use for empty regions
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/multiinter.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 <- get.random.regions(100, chr="chr1", sort = TRUE);

a.mult <- bedr.join.multiple.region(x = list(a.sort,b.sort,bedr.sort.region(d)));
}

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.