bedtools_unionbedg {HelloRanges} | R Documentation |
Summarize the ranges according to disjoin
and construct a matrix of scores (disjoint range by
sample/file). Empty cells are filled with NA
.
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)
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 |
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 |
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.
A language object containing the compiled R code, evaluating to a RangedSummarizedExperiment with an assay called “score”.
Michael Lawrence
http://bedtools.readthedocs.io/en/latest/content/tools/unionbedg.html
disjoin for forming disjoint ranges, RangedSummarizedExperiment-class for SummarizedExperiment objects.
## 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")