ranges-overlaps-self: Find overlaps within a Ranges object

In sa-lee/plyranges: A fluent interface for manipulating GenomicRanges

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.

Details

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

Value

a Ranges object

See Also

find_overlaps(), join_overlap_inner()

Examples

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)

sa-lee/plyranges documentation built on April 15, 2024, 12:25 p.m.