Find following Ranges
Ranges objects, which ranges in x follow those in y.
A character vector of length two used to identify metadata columns coming from x and y.
A Ranges object corresponding to the ranges in x`` that are followed by the ranges in y, all metadata is copied over from the right-hand side ranges y`.
By default join_follow will find abritrary ranges
in y that are followed by ranges in x and ignore any strand information.
On the other hand join_follow_left will find all ranges in y
that are on the left-hand side of the ranges in x ignoring any strand
information. Finally, join_follow_upstream will find all ranges in x
that are that are upstream of the ranges in y. On the positive strand this
will result in ranges in y that are left of those in x and on the negative
strand it will result in ranges in y that are right of those in x.
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()
join_follow(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 | 0.906426 a
#> [2] 10 14 5 | 0.389439 c
#> [3] 15 19 5 | 0.517460 e
#> [4] 20 24 5 | 0.125239 e
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_follow(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 91-101 - | b2 2 a1 1
#> [2] chr1 101-110 + | b3 3 a1 1
#> [3] chr1 201-210 - | b4 4 a2 2
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
join_follow_left(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 91-101 - | b2 2 a1 1
#> [2] chr1 101-110 + | b3 3 a1 1
#> [3] chr1 201-210 - | b4 4 a2 2
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
join_follow_upstream(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 101-110 + | b3 3 a1 1
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths