bt.shuffle: Randomly permute the locations of a feature file among a...

In PhanstielLab/bedtoolsr: Bedtools Wrapper

Randomly permute the locations of a feature file among a genome.

Description

Randomly permute the locations of a feature file among a genome.

Usage

bt.shuffle(
  i,
  g,
  excl = NULL,
  incl = NULL,
  chrom = NULL,
  seed = NULL,
  f = NULL,
  chromFirst = NULL,
  bedpe = NULL,
  maxTries = NULL,
  noOverlapping = NULL,
  allowBeyondChromEnd = NULL,
  output = NULL
)

Arguments

i	<bed/gff/vcf>
g	<genome>
excl	A BED/GFF/VCF file of coordinates in which features in -i should not be placed (e.g. gaps.bed).
incl	Instead of randomly placing features in a genome, the -incl options defines a BED/GFF/VCF file of coordinates in which features in -i should be randomly placed (e.g. genes.bed). Larger -incl intervals will contain more shuffled regions. This method DISABLES -chromFirst.
chrom	Keep features in -i on the same chromosome. - By default, the chrom and position are randomly chosen. - NOTE: Forces use of -chromFirst (see below).
seed	Supply an integer seed for the shuffling. - By default, the seed is chosen automatically. - (INTEGER)
f	Maximum overlap (as a fraction of the -i feature) with an -excl feature that is tolerated before searching for a new, randomized locus. For example, -f 0.10 allows up to 10 percent of a randomized feature to overlap with a given feature in the -excl file. **Cannot be used with -incl file.** - Default is 1E-9 (i.e., 1bp). - FLOAT (e.g. 0.50)
chromFirst	Instead of choosing a position randomly among the entire genome (the default), first choose a chrom randomly, and then choose a random start coordinate on that chrom. This leads to features being ~uniformly distributed among the chroms, as opposed to features being distribute as a function of chrom size.
bedpe	Indicate that the A file is in BEDPE format.
maxTries	Max. number of attempts to find a home for a shuffled interval in the presence of -incl or -excl. Default = 1000.
noOverlapping	Don't allow shuffled intervals to overlap.
allowBeyondChromEnd	Allow shuffled intervals to be relocated to a position in which the entire original interval cannot fit w/o exceeding the end of the chromosome. In this case, the end coordinate of the shuffled interval will be set to the chromosome's length. By default, an interval's original length must be fully-contained within the chromosome.
output	Output filepath instead of returning output in R.

PhanstielLab/bedtoolsr documentation built on Aug. 29, 2024, 5:37 p.m.