get_codon_usage_data: Get codon usage data (positional and bulk)

Description Usage Arguments Value Author(s) See Also

Description

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

Usage

1
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:

Author(s)

Dominique Sydow, [email protected]

See Also

create_html_report


ohlerlab/RiboseQC documentation built on May 9, 2019, 3:01 p.m.