bedtools_complement {HelloRanges} | R Documentation

## 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")

[Package HelloRanges version 1.16.0 Index]