bedtools_complement: bedtools_complement

In lawremi/HelloRanges: Introduce *Ranges to bedtools users

bedtools_complement

Description

Finds regions of the genome that are not covered by a genomic dataset.

Usage

bedtools_complement(cmd = "--help")
R_bedtools_complement(i, g)
do_bedtools_complement(i, g)

Arguments

cmd	String of bedtools command line arguments, as they would be entered at the shell. There are a few incompatibilities between the docopt parser and the bedtools style. See argument parsing.
i	Path to a BAM/BED/GFF/VCF/etc file, a BED stream, a file object, or a ranged data structure, such as a GRanges. Use "stdin" for input from another process (presumably while running via Rscript). For streaming from a subprocess, prefix the command string with “<”, e.g., "<grep foo file.bed". Any streamed data is assumed to be in BED format.
g	A genome file, identifier or Seqinfo object that defines the order and size of the sequences.

Details

As with all commands, there are three interfaces to the complement command:

bedtools_complement

Parses the bedtools command line and compiles it to the equivalent R code.

R_bedtools_complement

Accepts R arguments corresponding to the command line arguments and compiles the equivalent R code.

do_bedtools_complement

Evaluates the result of R_bedtools_complement. Recommended only for demonstration and testing. It is best to integrate the compiled code into an R script, after studying it.

The generated code is subtracts, via setdiff, the ranges from the set of ranges representing the entire genome.

While it may be tempting to call gaps instead, it is very unlikely to behave as expected. The GenomicRanges set operations treat all three strand values (+, -, *) as separate spaces. gaps takes as its universe the genome on all three strands, rather than just the “*” strand, resulting in extraneous stranded ranges.

Value

A language object containing the compiled R code, evaluating to a GRanges object with the complementary ranges.

Author(s)

Michael Lawrence

References

http://bedtools.readthedocs.io/en/latest/content/tools/complement.html

See Also

setops-methods for the various set operations.

Examples

## Not run: 
setwd(system.file("unitTests", "data", "coverage", package="HelloRanges"))

## End(Not run)
bedtools_complement("-i a.bed -g test.genome")

lawremi/HelloRanges documentation built on Oct. 29, 2023, 4:08 p.m.