est_trna_weight

<code>est_trna_weight</code> compute the tRNA weight per codon for TAI calculation.
This weight reflects relative tRNA availability for each codon.

A suite of functions for rapid and flexible analysis of codon
usage bias. It provides in-depth analysis at the codon level, including
relative synonymous codon usage (RSCU), tRNA weight calculations, machine
learning predictions for optimal or preferred codons, and visualization of
codon-anticodon pairing. Additionally, it can calculate various gene-
specific codon indices such as codon adaptation index (CAI), effective
number of codons (ENC), fraction of optimal codons (Fop), tRNA adaptation
index (tAI), mean codon stabilization coefficients (CSCg), and GC contents
(GC/GC3s/GC4d). It also supports both standard and non-standard genetic
code tables found in NCBI, as well as custom genetic code tables.

Hong Zhang

cubar

Codon Usage Bias Analysis

Mengyue Liu

Bu Zi

est_trna_weight function

<dl><dt>trna_level, </dt>
<dd>named vector of tRNA level (or gene copy numbers), one value for each anticodon.
vector names are anticodons.</dd>
<dt>codon_table</dt>
<dd>a table of genetic code derived from <code>get_codon_table</code> or <code>create_codon_table</code>.</dd>
<dt>s</dt>
<dd>list of non-Waston-Crick pairing panelty.</dd></dl>

Arguments

Estimate tRNA weight w — est_trna_weight

<dl>

<dt>trna_level, </dt>
<dd>named vector of tRNA level (or gene copy numbers), one value for each anticodon.
vector names are anticodons.</dd>


<dt>codon_table</dt>
<dd>a table of genetic code derived from <code>get_codon_table</code> or <code>create_codon_table</code>.</dd>


<dt>s</dt>
<dd>list of non-Waston-Crick pairing panelty.</dd>

</dl>

est_trna_weight: Estimate tRNA weight w

Description

Usage

Value

Arguments

References

Examples