get_codon_usage_data: Get codon usage data (positional and bulk)

In ohlerlab/RiboseQC: RiboseQC, a Comprehensive Ribo-Seq Analysis Tool

Get codon usage data (positional and bulk)

Description

This function processes codon usage data generated by RiboseQC_analysis, i.e. codon usage

• per nucleotide position (i.e. positional codon usage) as well as

• summed up over all positions* (i.e. bulk codon usage)

for a specific data type, originating compartment, and read length, as well as based on a user-defined genetic code.

This data is used as input in plot_codon_usage_bulk to generate a bar plot, and in plot_codon_usage_bulk_rmd to iterativly generate plots for the Ribo-seQC report in section 7.2.

Please check plot_codon_usage for positional codon usage (instead of bulk codon usage).

* Information on positions included in analysis:
Based on P-site corrected reads, the codon usage within CDS regions for protein coding genes is examplatory calculated

• for the first 11 codons of the CDS (referred to as start),

• for 11 codons from the middle of the CDS (referred to as middle), and

• for the last 11 codons of the CDS (referred to as stop).

Usage

get_codon_usage_data(data, data_type, comp, rl)

Arguments

data	Object (list of lists) generated by RiboseQC_analysis: res_all.
data_type	String; select one of the following: Codon_counts: codon count in defined positions*, P_sites_percodon: P-sites count in defined positions*, or P_sites_percodon_ratio: ratio of P-sites counts to codon counts in defined positions*. E_sites_percodon: E-sites count in defined positions*, or E_sites_percodon_ratio: ratio of E-sites counts to codon counts in defined positions*. A_sites_percodon: A-sites count in defined positions*, or A_sites_percodon_ratio: ratio of A-sites counts to codon counts in defined positions*.
comp	String for originating compartment. Check for available originating compartments in the data set using: names(res_all$profiles_P_sites$Codon_count)
rl	String for read length. Check for available read lengths in the data set using: names(res_all$profiles_P_sites[[data_type]][[comp]])

Value

This function returns a list (e.g. called codon_usage_bulk_data) with information on bulk codon usage:

• codon_usage_bulk_data$data contains the data on bulk codon usage,

• codon_usage_bulk_data$data_type saves the data type used (see parameter data_type)

• codon_usage_bulk_data$comp saves the originating compartment used (see parameter comp), and

• codon_usage_bulk_data$rl saves the read length used (see parameter rl).

Author(s)

Dominique Sydow, [e-mail]

See Also

create_html_report

ohlerlab/RiboseQC documentation built on Aug. 15, 2023, 7:30 a.m.