Finds regions of the genome that are not covered by a genomic dataset.
bedtools_complement(cmd = "--help") R_bedtools_complement(i, g) do_bedtools_complement(i, g)
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.
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
A genome file, identifier or Seqinfo object that defines the order and size of the sequences.
As with all commands, there are three interfaces to the
Parses the bedtools command line and compiles it to the equivalent R code.
Accepts R arguments corresponding to the command line arguments and compiles the equivalent R code.
Evaluates the result of
R_bedtools_complement. Recommended only for
demonstration and testing. It is best to integrate the compiled
code into an R script, after studying it.
The generated code is subtracts, via
setdiff, the ranges from the set of
ranges representing the entire genome.
While it may be tempting to call
instead, it is very unlikely to behave as expected. The GenomicRanges
set operations treat all three strand values (+, -, *) as separate
gaps takes as its universe the genome on all three
strands, rather than just the “*” strand, resulting in
extraneous stranded ranges.
A language object containing the compiled R code, evaluating to a GRanges object with the complementary ranges.
setops-methods for the various set operations.
## Not run: setwd(system.file("unitTests", "data", "coverage", package="HelloRanges")) ## End(Not run) bedtools_complement("-i a.bed -g test.genome")
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