Find preceding Ranges
Ranges objects, which ranges in x precede 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 y that are
preceded by the ranges in x, all metadata is copied over from the
right-hand side ranges y.
By default join_precede will return the ranges
in x that come before the ranges in y and ignore any strand information.
The function join_precede_right will find all ranges in y
that are on the right-hand side of the ranges in x ignoring any strand
information. Finally, join_precede_downstream will find all ranges in y
that are that are downstream of the ranges in x. On the positive strand this
will result in ranges in y that are right of those in x and on the negative
strand it will result in ranges in y that are left of those in x.
subject <- data.frame(start = c(5,10, 15,20), width = 5, gc = runif(4)) %>%
as_iranges()
query <- data.frame(start = 2:6, width = 3:7, label = letters[1:5]) %>%
as_iranges()
join_precede(query, subject)
#> IRanges object with 5 ranges and 2 metadata columns:
#> start end width | label gc
#> <integer> <integer> <integer> | <character> <numeric>
#> [1] 2 4 3 | a 0.9659899
#> [2] 3 6 4 | b 0.0376723
#> [3] 4 8 5 | c 0.0376723
#> [4] 5 10 6 | d 0.9164064
#> [5] 6 12 7 | e 0.9164064
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()
join_precede(query, subject)
#> GRanges object with 2 ranges and 4 metadata columns:
#> seqnames ranges strand | name.x score.x name.y score.y
#> <Rle> <IRanges> <Rle> | <character> <numeric> <character> <integer>
#> [1] chr1 11-21 + | a1 1 b2 2
#> [2] chr1 101-200 - | a2 2 b4 4
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
join_precede_right(query, subject)
#> GRanges object with 2 ranges and 4 metadata columns:
#> seqnames ranges strand | name.x score.x name.y score.y
#> <Rle> <IRanges> <Rle> | <character> <numeric> <character> <integer>
#> [1] chr1 11-21 + | a1 1 b2 2
#> [2] chr1 101-200 - | a2 2 b4 4
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
join_precede_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> <numeric> <character> <integer>
#> [1] chr1 11-21 + | a1 1 b3 3
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths