ranges-overlaps-self: Find overlaps within a Ranges object
In plyranges: A fluent interface for manipulating GenomicRanges

Description Usage Arguments Details Value See Also Examples

Find overlaps within a Ranges object

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)

`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.

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

a Ranges object

find_overlaps(), join_overlap_inner()

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)