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

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

Widen ranges on the left and/or right side.

bedtools_slop(cmd = "--help")
R_bedtools_slop(i, b = 0, l = 0, r = 0, s = FALSE, pct = FALSE,
                g = NULL, header = FALSE)
do_bedtools_slop(i, b = 0, l = 0, r = 0, s = FALSE, pct = FALSE,
                 g = NULL, header = FALSE)

`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.
`b`	Widen the same number base pairs in each direction.
`l`	The number of base pairs to subtract from the start coordinate.
`r`	The number of base pairs to add to the end coordinate.
`s`	Define `l` and `r` based on strand. For example. if `TRUE`, `l=500` for a negative-stranded feature will add 500 bp to the end coordinate.
`pct`	Define `l` and `r` as a fraction of the feature length. E.g. if used on a 1000bp feature, and `l` is 0.50, will add 500 bp upstream.
`g`	Genome file, identifier or Seqinfo object that defines the order and size of the sequences.
`header`	Ignored.

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

bedtools_slop: Parses the bedtools command line and compiles it to the equivalent R code.
R_bedtools_slop: Accepts R arguments corresponding to the command line arguments and compiles the equivalent R code.
do_bedtools_slop: Evaluates the result of R_bedtools_slop. Recommended only for demonstration and testing. It is best to integrate the compiled code into an R script, after studying it.

This is a fairly straight-forward application of resize and the + operator on GRanges.

A language object containing the compiled R code, evaluating to a GRanges, or similar, object. In principle, this is an endomorphism.

Michael Lawrence

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

intra-range-methods for resize.

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

## End(Not run)
## widen on both ends
bedtools_slop("-i a.bed -b 5 -g tiny.genome")
## widen only on the left end
bedtools_slop("-i a.bed -l 5 -r 0 -g tiny.genome")