plyranges (version 1.9.3)

join_overlap_self: Find overlaps within a Ranges object

Description

Find overlaps within a Ranges object

Usage

join_overlap_self(x, maxgap, minoverlap)
join_overlap_self_within(x, maxgap, minoverlap)
join_overlap_self_directed(x, maxgap, minoverlap)
join_overlap_self_within_directed(x, maxgap, minoverlap)

Arguments

x

A Ranges object

maxgap, minoverlap

The maximimum gap between intervals as an integer greater than or equal to zero. The minimum amount of overlap between intervals as an integer greater than zero, accounting for the maximum gap.

Value

a Ranges object

Details

Self overlaps find any overlaps (or overlaps within or overlaps directed) between a ranges object and itself.

See Also

find_overlaps(), join_overlap_inner()

Examples

# NOT RUN {
query <- data.frame(start = c(5,10, 15,20), width = 5, gc = runif(4)) %>%
             as_iranges()

join_overlap_self(query)

# -- GRanges objects, strand is ignored by default
query  <- data.frame(seqnames = "chr1",
               start = c(11,101),
               end = c(21, 200),
               name = c("a1", "a2"),
               strand = c("+", "-"),
               score = c(1,2)) %>%
           as_granges()

# ignores strandedness
join_overlap_self(query)
join_overlap_self_within(query)
# adding directed prefix includes strand
join_overlap_self_directed(query)


# }