bedtools_unionbedg {HelloRanges} | R Documentation

## bedtools_unionbedg

### Description

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

### Usage

        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)

### 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` | 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).

### Details

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.

### Value

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

### Author(s)

Michael Lawrence

### References

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

### See Also

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

### Examples

    ## 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")

[Package HelloRanges version 1.13.0 Index]