| join_overlap_intersect {plyranges} | R Documentation |
Join by overlapping Ranges
join_overlap_intersect(x, y, maxgap, minoverlap, suffix = c(".x", ".y"))
join_overlap_intersect_within(x, y, maxgap, minoverlap, suffix = c(".x",
".y"))
join_overlap_intersect_directed(x, y, maxgap, minoverlap, suffix = c(".x",
".y"))
join_overlap_intersect_within_directed(x, y, maxgap, minoverlap,
suffix = c(".x", ".y"))
join_overlap_inner(x, y, maxgap = -1L, minoverlap = 0L, suffix = c(".x",
".y"))
join_overlap_inner_within(x, y, maxgap = -1L, minoverlap = 0L,
suffix = c(".x", ".y"))
join_overlap_inner_directed(x, y, maxgap = -1L, minoverlap = 0L,
suffix = c(".x", ".y"))
join_overlap_inner_within_directed(x, y, maxgap = -1L, minoverlap = 0L,
suffix = c(".x", ".y"))
join_overlap_left(x, y, maxgap, minoverlap, suffix = c(".x", ".y"))
join_overlap_left_within(x, y, maxgap, minoverlap, suffix = c(".x", ".y"))
join_overlap_left_directed(x, y, maxgap, minoverlap, suffix = c(".x", ".y"))
join_overlap_left_within_directed(x, y, maxgap, minoverlap, suffix = c(".x",
".y"))
x, y |
Objects representing ranges |
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. |
suffix |
Character to vectors to append to common columns in x and y
(default = |
The function join_intersect_overlaps finds
the genomic intervals that are the overlapping ranges between x and y and
returns a new ranges object with metadata columns from x and y.
The function join_inner_overlaps is equivalent to find_overlaps.
The function join_left_overlaps performs a left outer join between x
and y. It returns all ranges in x that overlap or do not overlap ranges in y
plus metadata columns common to both. If there is no overlapping range
the metadata column will contain a missing value.
The function join_self_overlaps find all overlaps between a ranges
object x and itself.
All of these functions have two suffixes that modify their behavior.
The within suffix, returns only ranges in x that are completely
contained in y. The directed suffix takes into account the strandedness
of a GRanges object.
a GRanges object
x <- as_iranges(data.frame(start = c(11, 101), end = c(21, 201)))
y <- as_iranges(data.frame(start = c(10, 20, 50, 100),
end = c(19, 21, 105, 202)))
# intersect takes common interval
join_overlap_intersect(x,y)
# within
join_overlap_intersect_within(x,y)