generateSpace: Obtain the null distribution of a set of intervals

In leekgroup/enrichedRanges: Identify if a set of regions are enriched or not

Description

Given a set of regions of the genome, get random intervals for a number of permutations which will be used to determine the null distribution.

Usage

generateSpace(I, gr, nPermute = 1000, strand.specific = FALSE,
  randomize.strand = FALSE, seed = NULL)

Arguments

I	A GRanges object giving intervals from which to sample from.
gr	A GRanges object giving intervals of interest to resample from I.
nPermute	Number of permutations to run.
strand.specific	Whether the random intervals should have be strand specific or not.
randomize.strand	When strand.specific=TRUE, whether the strand should be randomized or depend on the strand from the regions in I.
seed	Seed to be used for reproducing the results.

Author(s)

Leonardo Collado-Torres

Examples

## Create some input ranges
library('GenomicRanges')
I <- GRanges(c('chr1', 'chrX'), IRanges(c(1e6, 3e6), width = 1e5), strand =
    c('+', '-'))
I

## Intervals of interest to resample from
gr <- GRanges(c('chr1', 'chrX'), IRanges(c(1e6, 3e6), width = 1e3), strand =
    c('+', '-'))
gr

## Set the seed if you want to reproduce the random results
set.seed(20140728)

## Obtain space of random intervals
space <- generateSpace(I, gr, nPermute = 1000)
space

leekgroup/enrichedRanges documentation built on June 6, 2019, 7:37 a.m.