bedtools_makewindows {HelloRanges} | R Documentation

## bedtools_makewindows

### Description

Generate a partitioning/tiling or set of sliding windows over the genome or a set of ranges.

### Usage

    bedtools_makewindows(cmd = "--help")
    R_bedtools_makewindows(b, g = NA_character_, w, s, n)
    do_bedtools_makewindows(b, g = NA_character_, w, s, n)

### 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.
`b` | 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. Windows are generated with each range. Exclusive with `g`.
`g` | A genome file, identifier or Seqinfo object that defines the order and size of the sequences. Specifying this generates windows over the genome. Exclusive with `b`.
`w` | Window size, exclusive with `n`.
`s` | Step size (generates sliding windows).
`n` | Number of windows, exclusive with `w`.

### Details

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

`bedtools_makewindows`

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

`R_bedtools_makewindows`

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

`do_bedtools_makewindows`

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

We view the generation of a partitioning (or tiling) as a distinct use case from the generation of sliding windows. The two use cases correspond to the `tile` and `slidingWindows` functions, respectively.

### Value

A language object containing the compiled R code, evaluating to a a GRangesList containing the windows for each range (or chromosome).

### Author(s)

Michael Lawrence

### References

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

### See Also

tile-methods for generating windows.

### Examples

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

    ## End(Not run)

    ## tiles of width 5000
    bedtools_makewindows("-b input.bed -w 5000")
    ## sliding windows, 5kb wide, every 2kb
    bedtools_makewindows("-b input.bed -w 5000 -s 2000")
    ## 3 tiles in each range
    bedtools_makewindows("-b input.bed -n 3")
    ## 3 tiles for each chromosome of the genome
    bedtools_makewindows("-g test.genome -n 3")

[Package HelloRanges version 1.12.0 Index]