random.intervals {seqbias} | R Documentation |
Given a vector of sequence lengths, generate genomic intervals uniformly at random
random.intervals(I, n=1, ms=10000)
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) |
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.
Returns a GRanges object giving the generated intervals.
Daniel Jones dcjones@cs.washington.edu
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 )