regionUpset — regionUpset • epiwraps

A wrapper around upset for comparing multiple sets of genomic ranges.

Usage

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

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 instead of plotting.
ignore.strand: Logical; whether to ignore strands when computing overlaps (default FALSE). Strand information is ignored if either of the compared sets of regions is unstranded.
maxgap: Maximum gap between regions to count as an overlap (see findOverlaps-methods).
minoverlap: Minimum overlap to count as a match (see findOverlaps-methods).
...: Further plotting arguments passed to upset.

A plot

# 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))
})
regionUpset(grl)