getStartStopWindows {ORFik} | R Documentation

## Get Start and Stop codon within specified windows over CDS.

### Description

For each cds in 'txdb' object, filtered by 'txNames', get a window around start and stop codons within 'window_size' downstream and upstream of the codon.

### Usage

    getStartStopWindows(txdb, txNames, start = TRUE, stop = TRUE,
      window_size = 30L, cds = NULL)

### Arguments

`txdb` | a txdb object of annotations
`txNames` | a character vector of the transcript names to use
`start` | (logical) whether to include start codons
`stop` | (logical) whether to incude stop codons
`window_size` | (integer) size of the window to extract upstream of the start/stop codon and downstream
`cds` | a GRangesList with cds, a speedup if you already have them loaded.

### Value

a list with two slots "starts" and "stops", each contains a GRangesList of windows around start and stop codons for the transcripts of interest

### Examples

    gtf_file <- system.file("extdata", "annotations.gtf", package = "ORFik")
    txdb <- GenomicFeatures::makeTxDbFromGFF(gtf_file, format = "gtf")
    txNames <- txNamesWithLeaders(txdb)
    getStartStopWindows(txdb, txNames)

[Package ORFik version 1.0.0 Index]