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

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

Summarize the ranges according to disjoin and construct a matrix of scores (disjoint range by sample/file). Empty cells are filled with NA.

    bedtools_unionbedg(cmd = "--help")
    R_bedtools_unionbedg(i, header=FALSE, names=NULL, g=NA_character_,
                          empty=FALSE)
    do_bedtools_unionbedg(i, header=FALSE, names=NULL, g=NA_character_,
                           empty=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`	Paths to BAM/BED/GFF/VCF/etc files (vector or comma-separated), or a list of objects.
`header`	Ignored.
`names`	Provide an alias for each to use for each `i` instead of their integer index. If a single string, can be comma-separated.
`g`	A genome file, identifier or Seqinfo object that defines the order and size of the sequences.
`empty`	Report empty regions (i.e., regions not covered in any of the files). This essentially yields a partitioning of the genome (and thus requires `g` to be specified).

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

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

This is essentially the same operation as bedtools_multiinter, except we build a score matrix and embed it into a SummarizedExperiment. This is a bit tricky and relies on the as.matrix,AtomicList-method coercion.

A language object containing the compiled R code, evaluating to a RangedSummarizedExperiment with an assay called “score”.

Michael Lawrence

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

disjoin for forming disjoint ranges, RangedSummarizedExperiment-class for SummarizedExperiment objects.

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

## End(Not run)

## combine three samples
bedtools_unionbedg("-i a.bedGraph,b.bedGraph,c.bedGraph -names A,B,C")
## include empty ranges (filled with NAs)
bedtools_unionbedg("-i a.bedGraph,b.bedGraph,c.bedGraph -names A,B,C -empty -g test.genome")