| randomize_regions {annotatr} | R Documentation |
randomize_regions is a wrapper function for regioneR::randomizeRegions() that simplifies the creation of randomized regions for an input set of regions read with read_regions(). It relies on the seqlengths of regions in order to build the appropriate genome object for regioneR::randomizeRegions().
randomize_regions(regions, allow.overlaps = TRUE, per.chromosome = TRUE, quiet = FALSE)
regions |
A |
allow.overlaps |
A logical stating whether random regions can overlap input regions (TRUE) or not (FALSE). Default TRUE. |
per.chromosome |
A logical stating whether the random regions should remain on the same chromosome (TRUE) or not (FALSE). Default TRUE. |
quiet |
Print progress messages (FALSE) or not (TRUE). |
NOTE: The data associated with the input regions are not passed on to the random regions.
A GRanges object of randomized regions based on regions from read_regions(). NOTE: Data associated with the original regions is not attached to the randomized regions.
# Create random region set based on ENCODE ChIP-seq data
file = system.file('extdata', 'Gm12878_Stat3_chr2.bed.gz', package = 'annotatr')
r = read_regions(con = file, genome = 'hg19')
random_r = randomize_regions(regions = r)