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

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

Compare two sets of genomic regions using the Jaccard statistic, defined as the total width of the intersection, divided by the total width of the union.

bedtools_jaccard(cmd = "--help")
R_bedtools_jaccard(a, b, f = 1e-09, F = 1e-09, r = FALSE, e = FALSE,
                   s = FALSE, S = FALSE, split = FALSE)
do_bedtools_jaccard(a, b, f = 1e-09, F = 1e-09, r = FALSE, e = FALSE,
                    s = FALSE, S = FALSE, split = 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.
`a`	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`	Like `a`, except supports multiple datasets, either as a vector/list or a comma-separated string. Also supports file glob patterns, i.e., strings containing the wildcard, “*”.
`f`	Minimum overlap required as a fraction of `a` [default: any overlap].
`F`	Minimum overlap required as a fraction of `b` [default: any overlap].
`r`	Require that the fraction of overlap be reciprocal for `a` and `b`. In other words, if `f` is 0.90 and `r` is `TRUE`, this requires that `b` overlap at least 90% of `a` and that `a` also overlaps at least 90% of `b`.
`e`	Require that the minimum fraction be satisfied for `a` OR `b`. In other words, if `e` is `TRUE` with `f=0.90` and `F=0.10` this requires that either 90% of `a` is covered OR 10% of `b` is covered. If `FALSE`, both fractions would have to be satisfied.
`s`	Require same strandedness. That is, find the jaccard feature in `b` that overlaps `a` on the same strand. By default, overlaps are reported without respect to strand. Note that this is the exact opposite of Bioconductor behavior.
`S`	Require opposite strandedness. That is, find the jaccard feature in `b` that overlaps `a` on the opposite strand. By default, overlaps are reported without respect to strand.
`split`	Treat split BAM (i.e., having an ‘N’ CIGAR operation) or BED12 entries as compound ranges with gaps, i.e., as GRangesList objects.

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

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

This is mostly just intersect and union, except when fractional overlap restrictions are involved.

A language object containing the compiled R code, evaluating to a a DataFrame with four columns:

`intersection`	total width of intersection
`union`	total width of union
`jaccard`	the jaccard statistic
`n_intersections`	the number of ranges representing the intersection

Michael Lawrence

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

setops-methods for set operations including intersect and union.

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

## End(Not run)

## basic
bedtools_jaccard("-a a.bed -b a.bed")
## excluding the gaps in compound ranges
bedtools_jaccard("-a three_blocks_match.bed -b e.bed -split")
## strand and fractional overlap restriction
bedtools_jaccard("-a aMixedStrands.bed -b bMixedStrands.bed -s -f 0.8")