Retreive a non-overlapping set of regions from a Genomic Ranges object

This function returns a GRanges object containing a non-overlapping set regions derived from a supplied Genomic Ranges object.

nonOverlappingGR(gr = NULL, by = "score", decreasing = TRUE, verbose = FALSE)

Arguments

gr

A GRanges object.

by

The name of a column in mcols(gr) that should be used to determine how overlapping regions should be resolved. The resolution of overlapping regions also depends on decreasing. For example, if a column named "score" is used for by, decreasing = TRUE means that the highest "score" in the overlap will be retained and decreasing = FALSE means that the lowest "score" in the overlap will be retained.

decreasing

A boolean value indicating whether the values in the column indicated via by should be ordered in decreasing order. If TRUE, the higher value in by will be retained.

verbose

A boolean value indicating whether the output should include extra reporting.

Examples

# Dummy GR
gr <- GRanges(
  seqnames = "chr1",
  ranges = IRanges(
    start = c(1, 4, 11),
    end = c(10, 12, 20)
  ),
  score = c(1, 2, 3)
)

# Non Overlapping
nonOverlappingGR(gr)