calculateOverlapSignificance-methods: function that calculates the significance of overlaps of two...
In genomation: Summary, annotation and visualization of genomic data

Description Usage Arguments Value

This function calculates the significance of overlaps of two sets of features using randomization. #' It returns a distributon of overlaps of a target set with a given randomized feature set. The randomization can be constrained by supplied arguments. The function is still in Beta mode - the regions can overlap excluded regions, and the randomized regions are not disjoint. Please take care that the excluded and included regions are not too strict when compared to the total width of the ranges.

calculateOverlapSignificance(target, feature, chrom.sizes = NULL,
  stranded = TRUE, keep.strand.prop = TRUE, keep.chrom = TRUE,
  exclude = NULL, include = NULL, seed = NULL, nrand = 1)

## S4 method for signature '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)

`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)