R/ranges-overlap-joins-intersect.R, R/ranges-overlap-joins-outer.R
overlap-joins.RdJoin 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")
)Objects representing ranges
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.
Character to vectors to append to common columns in x and y
(default = c(".x", ".y")).
a GRanges object
The function join_overlap_intersect() 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_overlap_inner() is equivalent to find_overlaps().
The function join_overlap_left() 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_overlap_self() 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
overlapped within in y. The directed suffix accounts for the strandedness
of the ranges when performing overlaps.
join_overlap_self(), join_overlap_left(), find_overlaps()
x <- as_iranges(data.frame(start = c(11, 101), end = c(21, 201)))
y <- as_iranges(data.frame(start = c(10, 20, 50, 100, 1),
end = c(19, 21, 105, 202, 5)))
# self
join_overlap_self(y)
#> IRanges object with 7 ranges and 0 metadata columns:
#> start end width
#> <integer> <integer> <integer>
#> [1] 10 19 10
#> [2] 20 21 2
#> [3] 50 105 56
#> [4] 50 105 56
#> [5] 100 202 103
#> [6] 100 202 103
#> [7] 1 5 5
# intersect takes common interval
join_overlap_intersect(x,y)
#> IRanges object with 4 ranges and 0 metadata columns:
#> start end width
#> <integer> <integer> <integer>
#> [1] 11 19 9
#> [2] 20 21 2
#> [3] 101 105 5
#> [4] 101 201 101
# within
join_overlap_intersect_within(x,y)
#> IRanges object with 1 range and 0 metadata columns:
#> start end width
#> <integer> <integer> <integer>
#> [1] 101 201 101
# left, and inner join, it's often useful having an id column here
y <- y %>% mutate(id = 1:n())
x <- x %>% mutate(id = 1:n())
join_overlap_inner(x,y)
#> IRanges object with 4 ranges and 2 metadata columns:
#> start end width | id.x id.y
#> <integer> <integer> <integer> | <integer> <integer>
#> [1] 11 21 11 | 1 1
#> [2] 11 21 11 | 1 2
#> [3] 101 201 101 | 2 3
#> [4] 101 201 101 | 2 4
join_overlap_left(y,x, suffix = c(".left", ".right"))
#> IRanges object with 5 ranges and 2 metadata columns:
#> start end width | id.left id.right
#> <integer> <integer> <integer> | <integer> <integer>
#> [1] 10 19 10 | 1 1
#> [2] 20 21 2 | 2 1
#> [3] 50 105 56 | 3 2
#> [4] 100 202 103 | 4 2
#> [5] 1 5 5 | 5 <NA>