convert2bed: convert object to bed format

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

Description

checks if an object can be converted into a bed style data.frame then does the conversion.

Usage

convert2bed(
	x,
	set.type = TRUE,
	check.zero.based = TRUE,
	check.chr = TRUE,
	check.valid = TRUE,
	check.sort = TRUE,
	check.merge = TRUE,
	verbose = TRUE
	)

Arguments

x	A region index (i.e. chr1:10-100, ...) either as a vector or row.names/first column of a data.frame. Or a data.frame with the first three columns "chr", s"start", "end"
set.type	should the attribute input.type be set. Sometimes it is desirable to avoid setting it when applying intermediate conversion
check.zero.based	should 0 based coordinates be checked
check.chr	should chr prefix be checked
check.valid	should the region be checked for integerity
check.sort	should the region be checked to see if it is sorted
check.merge	should the region be checked for overlapping regions
verbose	messages and text

Details

Very useful to convert data before using other bedr functions

Value

Returns x converted to bedformat, as a data frame

Author(s)

Daryl Waggott

Examples

## Not run: 
  a.bed <- convert.to.bed(a) 
  
## End(Not run)

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