Usage
calculateOverlapSignificance(target, feature, chrom.sizes = NULL,
stranded = TRUE, keep.strand.prop = TRUE, keep.chrom = TRUE,
exclude = NULL, include = NULL, seed = NULL, nrand = 1)## S3 method for class 'GRanges,GRanges':
calculateOverlapSignificance(target, feature,
chrom.sizes = NULL, stranded = TRUE, keep.strand.prop = TRUE,
keep.chrom = TRUE, exclude = NULL, include = NULL, seed = NULL,
nrand = 1)
Arguments
target
a GRanges object for which the overlap needs to be calculates
feature
a GRanges object to be randomized
chrom.sizes
sizes of chromosomes as a named vector (names are
chromsomes names and elements of the vectors are lengths). , if not
given sizes in GRanges object will be used if no sizes there the end
of each chr will be the end last feature on each chr
stranded
if FALSE, all of the returned features will be strandless
(will have "*" in the strand slot)
keep.strand.prop
If TRUE strands will have the same proportion as the
features
keep.chrom
If TRUE, number of features and randomized features for a
chromosome will match. Currently seeting this to FALSE is not supported.
exclude
A GRanges object where no randomized feature should overlap,
can be gaps or unmappable regions in the genome as an example.
include
A GRanges object which defines the boundaries of randomized
features
seed
random number generator seed
nrand
number of randomizations (default:1)