get_cds_codons: Get A Granges object with locations of each codon in the...

View source: R/kl_div.R

get_cds_codonsR Documentation

Get A Granges object with locations of each codon in the given cds

Description

Get A Granges object with locations of each codon in the given cds

Usage

get_cds_codons(
  anno,
  n_wind_l_ext = 45,
  n_wind_r_ext = 9,
  n_start_buff = 60,
  n_end_buff = 60
)

Arguments

anno

An annotation object

n_wind_l_ext

The 5' extent of the window around the codon to return Defaults to: 45

n_wind_r_ext

The 3' extent of the window around the codon to return Defaults to: 9

n_start_buff

The number of bp at the start of each cds to exclude Defaults to 60

n_end_buff

The number of bp at the end of each cds to exclude Defaults to 60

Details

Use estimates of per codon dwell time to get the mean dwell time over transcrips

Value

a GRanges object with the codon identity in the names, and the

Author(s)

Dermot Harnett, dermot.p.harnett@gmail.com


zslastman/RiboStan documentation built on June 12, 2024, 1:59 a.m.