startSites {ORFik} | R Documentation

## 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` | if asGR is False, do you still want to keep a named vector
`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)

[Package ORFik version 1.2.1 Index]