ranges-nearest: Find nearest neighbours between two Ranges objects

In sa-lee/plyranges: A fluent interface for manipulating GenomicRanges

Find nearest neighbours between two Ranges objects

Description

Find nearest neighbours between two Ranges objects

Usage

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)

Arguments

x, y	Ranges objects, add the nearest neighbours of ranges in x to those in y.
suffix	A character vector of length two used to identify metadata columns
distance	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.

Details

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.

Value

A Ranges object corresponding to the nearest ranges, all metadata is copied over from the right-hand side ranges y.

Examples

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)
join_nearest_left(query, subject)
join_nearest_right(query, subject)

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)
join_nearest_downstream(query, subject)

sa-lee/plyranges documentation built on April 15, 2024, 12:25 p.m.