bedtools_makewindows: bedtools_makewindows
In HelloRanges: Introduce *Ranges to bedtools users

Description Usage Arguments Details Value Author(s) References See Also Examples

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

1
2
3

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

`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`.

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.

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

Michael Lawrence

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

tile-methods for generating windows.

## 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")