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 1.30.0 Index]