tile1: Tile each GRangesList group to 1-base resolution.

In JokingHero/ORFik: Open Reading Frames in Genomics

Tile each GRangesList group to 1-base resolution.

Description

Will tile a GRangesList into single bp resolution, each group of the list will be splited by positions of 1. Returned values are sorted as the same groups as the original GRangesList, except they are in bp resolutions. This is not supported originally by GenomicRanges for GRangesList.

Usage

tile1(grl, sort.on.return = TRUE, matchNaming = TRUE, is.sorted = TRUE)

Arguments

grl	a GRangesList object with names.
sort.on.return	logical (TRUE), should the groups be sorted before return (Negative ranges should be in decreasing order). Makes it a bit slower, but much safer for downstream analysis.
matchNaming	logical (TRUE), should groups keep unlisted names and meta data.(This make the list very big, for > 100K groups)
is.sorted	logical (TRUE), grl is presorted (negative coordinates are decreasing). Set to FALSE if they are not, else output will most likely be wrong!

Value

a GRangesList grouped by original group, tiled to 1. Groups with identical names will be merged.

See Also

Other ExtendGenomicRanges: asTX(), coveragePerTiling(), extendLeaders(), extendTrailers(), reduceKeepAttr(), txSeqsFromFa(), windowPerGroup()

Examples

gr1 <- GRanges("1", ranges = IRanges(start = c(1, 10, 20),
                                     end = c(5, 15, 25)),
               strand = "+")
gr2 <- GRanges("1", ranges = IRanges(start = c(20, 30, 40),
                                     end = c(25, 35, 45)),
               strand = "+")
names(gr1) = rep("tx1_1", 3)
names(gr2) = rep("tx1_2", 3)
grl <- GRangesList(tx1_1 = gr1, tx1_2 = gr2)
tile1(grl)

JokingHero/ORFik documentation built on Oct. 21, 2024, 11:42 a.m.