R/ranges-add-distance.R
add-nearest-distance.RdAppends 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.
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")The query ranges
the subject ranges within which the nearest ranges are found. If missing, query ranges are used as the subject.
column name to create containing distance values
ranges in x with additional column containing the distance to the
nearest range in y.
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.
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)
#> IRanges object with 4 ranges and 2 metadata columns:
#> start end width | gc distance
#> <integer> <integer> <integer> | <numeric> <integer>
#> [1] 5 9 5 | 0.0807501 0
#> [2] 10 14 5 | 0.8343330 0
#> [3] 15 19 5 | 0.6007609 2
#> [4] 20 24 5 | 0.1572084 0
add_nearest_distance_left(query, subject)
#> IRanges object with 4 ranges and 2 metadata columns:
#> start end width | gc distance
#> <integer> <integer> <integer> | <numeric> <integer>
#> [1] 5 9 5 | 0.0807501 0
#> [2] 10 14 5 | 0.8343330 0
#> [3] 15 19 5 | 0.6007609 2
#> [4] 20 24 5 | 0.1572084 <NA>
add_nearest_distance_left(query)
#> IRanges object with 4 ranges and 2 metadata columns:
#> start end width | gc distance
#> <integer> <integer> <integer> | <numeric> <integer>
#> [1] 5 9 5 | 0.0807501 <NA>
#> [2] 10 14 5 | 0.8343330 0
#> [3] 15 19 5 | 0.6007609 0
#> [4] 20 24 5 | 0.1572084 0