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

In zslastman/RiboStan: Estimates Isoform Specific RPF Footprint Densities

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, [e-mail]

zslastman/RiboStan documentation built on April 6, 2024, 1:35 p.m.