Description Usage Arguments Details Value Author(s) References See Also Examples
Compute flanking regions.
1 2 3 4 5 | bedtools_flank(cmd = "--help")
R_bedtools_flank(i, b = 0, l = 0, r = 0, s = FALSE, pct = FALSE,
g = NULL, header = FALSE)
do_bedtools_flank(i, b = 0, l = 0, r = 0, s = FALSE, pct = FALSE,
g = NULL, header = 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 |
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 |
b |
Increase the BED/GFF/VCF range by the same number base pairs in each direction. Integer. |
l |
The number of base pairs to subtract from the start coordinate. Integer. |
r |
The number of base pairs to add to the end coordinate. Integer. |
s |
Define |
pct |
Define |
g |
Genome file, identifier or Seqinfo object that defines the order and size of the sequences. |
header |
Ignored. |
As with all commands, there are three interfaces to the
flank
command:
bedtools_flank
Parses the bedtools command line and compiles it to the equivalent R code.
R_bedtools_flank
Accepts R arguments corresponding to the command line arguments and compiles the equivalent R code.
do_bedtools_flank
Evaluates the result of
R_bedtools_flank
. Recommended only for
demonstration and testing. It is best to integrate the compiled
code into an R script, after studying it.
We compute the flanks with flank
,
although flank
only computes one side at a time, so we may call
it multiple times.
A language object containing the compiled R code, evaluating to a GRanges object.
Michael Lawrence
http://bedtools.readthedocs.io/en/latest/content/tools/flank.html
intra-range-methods for flank
.
1 2 3 4 5 6 7 8 9 10 | ## Not run:
setwd(system.file("unitTests", "data", "flank", package="HelloRanges"))
## End(Not run)
## 5 on both sides
r <- bedtools_flank("-i a.bed -b 5 -g tiny.genome")
## 5 on left side
bedtools_flank("-i a.bed -l 5 -r 0 -g tiny.genome")
## define left/right in terms of transcription direction
bedtools_flank("-i a.bed -l 5 -r 0 -s -g tiny.genome")
|
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