R/ranges-overlap-find.R, R/ranges-overlap-groups.R
ranges-overlaps.RdFind overlap between two Ranges
find_overlaps(x, y, maxgap, minoverlap, suffix = c(".x", ".y"))
# S3 method for IntegerRanges
find_overlaps(x, y, maxgap = -1L, minoverlap = 0L, suffix = c(".x", ".y"))
# S3 method for GenomicRanges
find_overlaps(x, y, maxgap = -1L, minoverlap = 0L, suffix = c(".x", ".y"))
find_overlaps_within(x, y, maxgap, minoverlap, suffix = c(".x", ".y"))
# S3 method for IntegerRanges
find_overlaps_within(
x,
y,
maxgap = -1L,
minoverlap = 0L,
suffix = c(".x", ".y")
)
# S3 method for GenomicRanges
find_overlaps_within(
x,
y,
maxgap = -1L,
minoverlap = 0L,
suffix = c(".x", ".y")
)
find_overlaps_directed(x, y, maxgap, minoverlap, suffix = c(".x", ".y"))
# S3 method for GenomicRanges
find_overlaps_directed(
x,
y,
maxgap = -1L,
minoverlap = 0L,
suffix = c(".x", ".y")
)
find_overlaps_within_directed(x, y, maxgap, minoverlap, suffix = c(".x", ".y"))
# S3 method for GenomicRanges
find_overlaps_within_directed(x, y, maxgap, minoverlap, suffix = c(".x", ".y"))
group_by_overlaps(x, y, maxgap, minoverlap)
# S3 method for IntegerRanges
group_by_overlaps(x, y, maxgap = -1L, minoverlap = 0L)
# S3 method for GenomicRanges
group_by_overlaps(x, y, maxgap = -1L, minoverlap = 0L)Objects representing ranges
The maximimum gap between intervals as an integer greater than or equal to negative one. The minimum amount of overlap between intervals as an integer greater than zero, accounting for the maximum gap.
A character vector of length two used to identify metadata columns coming from x and y.
A Ranges object with rows corresponding to the
ranges in x that overlap y. In the case of group_by_overlaps(), returns
a GroupedRanges object, grouped by the number of overlaps
of ranges in x that overlap y (stored in a column called query).
find_overlaps() will search for any overlaps between ranges
x and y and return a Ranges object of length equal to the number of times x
overlaps y. This Ranges object will have additional metadata columns
corresponding to the metadata columns in y. find_overlaps_within() is
the same but will only search for overlaps within y. For GRanges objects strand is
ignored, unless find_overlaps_directed() is used. If the Ranges objects have no
metadata, one could use group_by_overlaps() to be able to
identify the index of the input Range x that overlaps a Range in y.
Alternatively,
pair_overlaps() could be used to place the x ranges next to the range
in y they overlap.
IRanges::findOverlaps(),
GenomicRanges::findOverlaps()
query <- data.frame(start = c(5,10, 15,20), width = 5, gc = runif(4)) %>%
as_iranges()
subject <- data.frame(start = 2:6, width = 3:7, label = letters[1:5]) %>%
as_iranges()
find_overlaps(query, subject)
#> IRanges object with 6 ranges and 2 metadata columns:
#> start end width | gc label
#> <integer> <integer> <integer> | <numeric> <character>
#> [1] 5 9 5 | 0.971117 b
#> [2] 5 9 5 | 0.971117 c
#> [3] 5 9 5 | 0.971117 d
#> [4] 5 9 5 | 0.971117 e
#> [5] 10 14 5 | 0.701959 d
#> [6] 10 14 5 | 0.701959 e
find_overlaps(query, subject, minoverlap = 5)
#> IRanges object with 1 range and 2 metadata columns:
#> start end width | gc label
#> <integer> <integer> <integer> | <numeric> <character>
#> [1] 5 9 5 | 0.971117 d
find_overlaps_within(query, subject) # same result as minoverlap
#> IRanges object with 1 range and 2 metadata columns:
#> start end width | gc label
#> <integer> <integer> <integer> | <numeric> <character>
#> [1] 5 9 5 | 0.971117 d
find_overlaps(query, subject, maxgap = 1)
#> IRanges object with 8 ranges and 2 metadata columns:
#> start end width | gc label
#> <integer> <integer> <integer> | <numeric> <character>
#> [1] 5 9 5 | 0.971117 a
#> [2] 5 9 5 | 0.971117 b
#> [3] 5 9 5 | 0.971117 c
#> [4] 5 9 5 | 0.971117 d
#> [5] 5 9 5 | 0.971117 e
#> [6] 10 14 5 | 0.701959 c
#> [7] 10 14 5 | 0.701959 d
#> [8] 10 14 5 | 0.701959 e
# -- 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()
subject <- data.frame(seqnames = "chr1",
strand = c("+", "-", "+", "-"),
start = c(21,91,101,201),
end = c(30,101,110,210),
name = paste0("b", 1:4),
score = 1:4) %>%
as_granges()
# ignores strandedness
find_overlaps(query, subject, suffix = c(".query", ".subject"))
#> GRanges object with 3 ranges and 4 metadata columns:
#> seqnames ranges strand | name.query score.query name.subject
#> <Rle> <IRanges> <Rle> | <character> <numeric> <character>
#> [1] chr1 11-21 + | a1 1 b1
#> [2] chr1 101-200 - | a2 2 b2
#> [3] chr1 101-200 - | a2 2 b3
#> score.subject
#> <integer>
#> [1] 1
#> [2] 2
#> [3] 3
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
find_overlaps(query, subject, suffix = c(".query", ".subject"), minoverlap = 2)
#> GRanges object with 1 range and 4 metadata columns:
#> seqnames ranges strand | name.query score.query name.subject
#> <Rle> <IRanges> <Rle> | <character> <numeric> <character>
#> [1] chr1 101-200 - | a2 2 b3
#> score.subject
#> <integer>
#> [1] 3
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
# adding directed prefix includes strand
find_overlaps_directed(query, subject, suffix = c(".query", ".subject"))
#> GRanges object with 2 ranges and 4 metadata columns:
#> seqnames ranges strand | name.query score.query name.subject
#> <Rle> <IRanges> <Rle> | <character> <numeric> <character>
#> [1] chr1 11-21 + | a1 1 b1
#> [2] chr1 101-200 - | a2 2 b2
#> score.subject
#> <integer>
#> [1] 1
#> [2] 2
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths