Summarize the ranges according to
and annotate each disjoint range with the samples that overlap the
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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.
Paths to BAM/BED/GFF/VCF/etc files (vector or comma-separated), or a list of objects.
Provide an alias for each to use for each
A genome file, identifier or Seqinfo object that defines the order and size of the sequences.
Report empty regions (i.e., regions not covered in any of the
files). This essentially yields a partitioning of the genome (and
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_multiinter. Recommended only for
demonstration and testing. It is best to integrate the compiled
code into an R script, after studying it.
The workhorse is
disjoin causes it to return a list of integers, which we use
to extract the sample identifiers. The
empty case requires a
bit more code, because we have to combine the disjoint ranges with the
A language object containing the compiled R code, evaluating to a GRanges with a column “i” indicating the sample memberships.
disjoin for forming disjoint ranges.
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## Not run: setwd(system.file("unitTests", "data", "multiinter", package="HelloRanges")) ## End(Not run) ## default behavior bedtools_multiinter("-i a.bed,b.bed,c.bed") ## custom names bedtools_multiinter("-i a.bed,b.bed,c.bed -names A,B,C") ## include empty regions, i.e., partition the genome bedtools_multiinter("-i a.bed,b.bed,c.bed -names A,B,C -empty -g test.genome")
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