regionsToUpset

Prepares sets of regions for UpSet overlap representation.

Usage

regionsToUpset(
  x,
  reference = c("reduce", "disjoin"),
  returnList = FALSE,
  ignore.strand = FALSE,
  maxgap = -1L,
  minoverlap = 0L,
  ...
)

Arguments

x

A named list of genomic ranges (or paths to bed files)

reference

The method for creating the reference windows ('reduce' or 'disjoin'). Alternatively, a `GRanges` object of reference windows.

returnList

Logical; whether to return the list of regions instead of plotting.

ignore.strand

Logical; whether to ignore strand for overlaps (default FALSE).

maxgap

Max gap between regions to consider an overlap.

minoverlap

Minimum number of overlapping bases.

...

Further arguments specifying how the overlaps are done, passed to findOverlaps-methods).

Value

A data.frame of set inclusions which can be directly input to make_comb_mat, and then UpSet.

Examples

# random list of GRanges:
grl <- lapply(c(A=10,B=20,C=30), FUN=function(x){
  GRanges("seq1", IRanges(runif(x,1,1000), width=20))
})
input_for_upset <- regionsToUpset(grl)
# we would then plot the data with:
ComplexHeatmap::UpSet(make_comb_mat(input_for_upset))