ranges-follow: Find following Ranges

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

Find following Ranges

Description

Find following Ranges

Usage

join_follow(x, y, suffix = c(".x", ".y"))

join_follow_left(x, y, suffix = c(".x", ".y"))

join_follow_upstream(x, y, suffix = c(".x", ".y"))

Arguments

x, y	Ranges objects, which ranges in x follow those in y.
suffix	A character vector of length two used to identify metadata columns coming from x and y.

Details

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.

Value

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'.

Examples

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)

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)
join_follow_left(query, subject)
join_follow_upstream(query, subject)

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