add-nearest-distance: Add distance to nearest neighbours between two Ranges objects

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

Add distance to nearest neighbours between two Ranges objects

Description

Appends distance to nearest subject range to query ranges similar to setting distance in join_nearest_. Distance is set to NA for features with no nearest feature by the selected nearest metric.

Usage

add_nearest_distance(x, y = x, name = "distance")

add_nearest_distance_left(x, y = x, name = "distance")

add_nearest_distance_right(x, y = x, name = "distance")

add_nearest_distance_upstream(x, y = x, name = "distance")

add_nearest_distance_downstream(x, y = x, name = "distance")

Arguments

x	The query ranges
y	the subject ranges within which the nearest ranges are found. If missing, query ranges are used as the subject.
name	column name to create containing distance values

Details

By default add_nearest_distance will find arbitrary nearest neighbours in either direction and ignore any strand information. The add_nearest_distance_left and add_nearest_distance_right methods will find arbitrary nearest neighbour ranges on x that are left/right of those on y and ignore any strand information.

The add_nearest_distance_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 add_nearest_distance_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

ranges in x with additional column containing the distance to the nearest range in y.

See Also

join_nearest

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()
             
add_nearest_distance(query, subject)
add_nearest_distance_left(query, subject)
add_nearest_distance_left(query)

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