bedr (version 1.0.7)

convert2bed: convert object to bed format

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
	)

Value

Returns x converted to bedformat, as a data frame

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

Author

Daryl Waggott

Details

Very useful to convert data before using other bedr functions

Examples

if (FALSE) {
  a.bed <- convert.to.bed(a) 
  }