regionsToUpset

Prepares sets of regions for UpSet overlap representation. A wrapper around upset for comparing multiple sets of genomic ranges.

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.

...

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)))
#> Error in ComplexHeatmap(UpSet(make_comb_mat(input_for_upset))): could not find function "ComplexHeatmap"