Summarize the ranges according to
and construct a matrix of scores (disjoint range by
sample/file). Empty cells are filled with
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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_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
A language object containing the compiled R code, evaluating to a RangedSummarizedExperiment with an assay called “score”.
disjoin for forming disjoint ranges, RangedSummarizedExperiment-class for SummarizedExperiment objects.
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## 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")
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