random.intervals {seqbias}R Documentation

Generating random genomic intervals

Description

Given a vector of sequence lengths, generate genomic intervals uniformly at random

Usage

random.intervals(I, n=1, ms=10000)

Arguments

I

a GRanges object giving intervals from which to sample from

n

number of intervals to generate

ms

length of the intervals to generate (may be a vector)

Details

The function is used to place intervals of fixed sizes at random (possibly overlapping) positions across one or more sequences. The input should be a GRanges objects giving the sequence intervals in which the random intervals sholud be placed. If they are to be placed anywhere within a reference sequence, use the scanFaIndex function from Rsamtools, to obtain a set of intervals.

Value

Returns a GRanges object giving the generated intervals.

Author(s)

Daniel Jones dcjones@cs.washington.edu

Examples

  library(Rsamtools)
  ref_fn <- system.file( "extra/example.fa", package = "seqbias" )
  ref_f <- FaFile( ref_fn )
  open.FaFile( ref_f )

  ref_seqs <- scanFaIndex( ref_f )

  I <- random.intervals( ref_seqs, n = 100, ms = 1000 )

[Package seqbias version 1.28.0 Index]