bed_to_granges: BED to GRanges

In carjed/smaug: Helper functions for the SMAUG pipeline

Description

This function loads a BED-like file and stores it as a GRanges object. The tab-delimited file must be ordered as 'chr', 'start', 'end', 'id', 'score', 'strand'. The minimal BED file must have the 'chr', 'start', 'end' columns. Any columns after the strand column are ignored.

Usage

bed_to_granges(file, header)

Arguments

file	Location of your file
header	logical; indicates whether or not bed file has a header

Details

This is a forked version of the function written by Dave Tang (https://github.com/davetang/bedr), with added support for bed files with headers

Examples

bed_to_granges('my_bed_file.bed')

carjed/smaug documentation built on May 5, 2019, 3:49 a.m.