seqbias (version 1.20.0)

random.intervals: 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)

Value

Returns a GRanges object giving the generated intervals.

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.

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 )