R/ranges-join-nearest.R
ranges-nearest.RdFind nearest neighbours between two Ranges objects
join_nearest(x, y, suffix = c(".x", ".y"), distance = FALSE)
join_nearest_left(x, y, suffix = c(".x", ".y"), distance = FALSE)
join_nearest_right(x, y, suffix = c(".x", ".y"), distance = FALSE)
join_nearest_upstream(x, y, suffix = c(".x", ".y"), distance = FALSE)
join_nearest_downstream(x, y, suffix = c(".x", ".y"), distance = FALSE)Ranges objects, add the nearest neighbours of ranges in x to those in y.
A character vector of length two used to identify metadata columns
logical vector whether to add a column named "distance" containing the distance to the nearest region. If set to a character vector of length 1, will use that as distance column name.
A Ranges object corresponding to the nearest ranges, all metadata
is copied over from the right-hand side ranges y.
By default join_nearest will find arbitrary nearest
neighbours in either direction and ignore any strand information.
The join_nearest_left and join_nearest_right methods
will find arbitrary nearest neighbour ranges on x that are left/right of
those on y and ignore any strand information.
The join_nearest_upstream method will find arbitrary nearest
neighbour ranges on x that are upstream of those on y. This takes into
account strandedness of the ranges.
On the positive strand nearest upstream will be on the
left and on the negative strand nearest upstream will be on the right.
The join_nearest_downstream method will find arbitrary nearest
neighbour ranges on x that are upstream of those on y. This takes into
account strandedness of the ranges.On the positive strand nearest downstream
will be on the right and on the negative strand nearest upstream will be on
the left.
query <- data.frame(start = c(5,10, 15,20),
width = 5,
gc = runif(4)) %>%
as_iranges()
subject <- data.frame(start = c(2:6, 24),
width = 3:8,
label = letters[1:6]) %>%
as_iranges()
join_nearest(query, subject)
#> IRanges object with 4 ranges and 2 metadata columns:
#> start end width | gc label
#> <integer> <integer> <integer> | <numeric> <character>
#> [1] 5 9 5 | 0.0301457 e
#> [2] 10 14 5 | 0.7718055 e
#> [3] 15 19 5 | 0.3274151 e
#> [4] 20 24 5 | 0.3894787 f
join_nearest_left(query, subject)
#> IRanges object with 3 ranges and 2 metadata columns:
#> start end width | gc label
#> <integer> <integer> <integer> | <numeric> <character>
#> [1] 5 9 5 | 0.0301457 a
#> [2] 10 14 5 | 0.7718055 d
#> [3] 15 19 5 | 0.3274151 e
join_nearest_right(query, subject)
#> IRanges object with 1 range and 2 metadata columns:
#> start end width | gc label
#> <integer> <integer> <integer> | <numeric> <character>
#> [1] 20 24 5 | 0.389479 f
subject <- data.frame(seqnames = "chr1",
start = c(11,101),
end = c(21, 200),
name = c("a1", "a2"),
strand = c("+", "-"),
score = c(1,2)) %>%
as_granges()
query <- 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()
join_nearest_upstream(query, subject)
#> GRanges object with 3 ranges and 4 metadata columns:
#> seqnames ranges strand | name.x score.x name.y score.y
#> <Rle> <IRanges> <Rle> | <character> <integer> <character> <numeric>
#> [1] chr1 21-30 + | b1 1 a1 1
#> [2] chr1 91-101 - | b2 2 a2 2
#> [3] chr1 101-110 + | b3 3 a1 1
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
join_nearest_downstream(query, subject)
#> GRanges object with 1 range and 4 metadata columns:
#> seqnames ranges strand | name.x score.x name.y score.y
#> <Rle> <IRanges> <Rle> | <character> <integer> <character> <numeric>
#> [1] chr1 201-210 - | b4 4 a2 2
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths