startSites: Get the start sites from a GRangesList of orfs grouped by...

In JokingHero/ORFik: Open Reading Frames in Genomics

Get the start sites from a GRangesList of orfs grouped by orfs

Description

In ATGTTTTGG, get the position of the A.

Usage

startSites(grl, asGR = FALSE, keep.names = FALSE, is.sorted = FALSE)

Arguments

grl	a GRangesList object
asGR	a boolean, return as GRanges object
keep.names	a logical (FALSE), keep names of input.
is.sorted	a speedup, if you know the ranges are sorted

Value

if asGR is False, a vector, if True a GRanges object

See Also

Other ORFHelpers: defineTrailer(), longestORFs(), mapToGRanges(), orfID(), startCodons(), stopCodons(), stopSites(), txNames(), uniqueGroups(), uniqueOrder()

Examples

gr_plus <- GRanges(seqnames = c("chr1", "chr1"),
                   ranges = IRanges(c(7, 14), width = 3),
                   strand = c("+", "+"))
gr_minus <- GRanges(seqnames = c("chr2", "chr2"),
                    ranges = IRanges(c(4, 1), c(9, 3)),
                    strand = c("-", "-"))
grl <- GRangesList(tx1 = gr_plus, tx2 = gr_minus)
startSites(grl, is.sorted = FALSE)

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