extendLeadersUntil: Extend Leaders Until

In JokingHero/ORFik: Open Reading Frames in Genomics

Extend Leaders Until

Description

Extend leaders until a restriction group / position. This makes you extend until you hit another gene boundary etc.

Usage

extendLeadersUntil(
  grl,
  grl2 = grl,
  extension = 500,
  until = 200,
  min_ext = 25,
  is.circular = all(isCircular(grl) %in% TRUE),
  ...
)

Arguments

grl	a GRangesList
grl2	a GRangesList, default 'grl'. The list that defines restrictions on extension. Can also be another set, which is used as 'roadblocks' for extension.
extension	an integer, how much to max extend upstream (5' end). Either single value that will apply for all, or same as length of grl which will give 1 update value per grl object. Or a GRangesList where start / stops by strand are the positions to use as new starts. Will not cross the chromosome boundary for non circular chromosomes.
until	numeric, default 200. The nearest you can go to the neighbour boundaries of grl2 (the "other" genes). Defined as boundary hit + 1, so if hit other gene with distance 22, and 'until' argument is 2, will set final extension to 22-2-1 = 19. Usually if Leaders/trailers are not defined, this makes a good pseudo leader boundary around your other genes.
min_ext	numeric, default 25. What is the minimum extension, even though it crosses a boundary. Will not cross the chromosome boundary for non circular chromosomes.
is.circular	logical, default FALSE if not any is: all(isCircular(grl) Where grl is the ranges checked. If TRUE, allow ranges to extend below position 1 on chromosome. Since circular genomes can have negative coordinates.
...	Arguments sent to distanceToPreceding

Value

a GRangesList of extended grl input

Examples

grl <- GRangesList(tx1 = GRanges("1", IRanges(c(10, 15), c(13, 20)), "+"),
                   tx2 = GRanges("1", IRanges(30, 50), "+"))
extendLeadersUntil(grl, min_ext = 5)
extendLeadersUntil(grl, min_ext = 5, until = 1)
extendLeadersUntil(grl, min_ext = 5, until = 1)
extendLeadersUntil(grl, min_ext = 5, until = 1, extension = 4)

JokingHero/ORFik documentation built on Dec. 21, 2024, 12:01 a.m.