get_fop

<code>get_fop</code> calculates the fraction of optimal codons (Fop) of each CDS.

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

get_fop function

<dl><dt>cf</dt>
<dd>matrix of codon frequencies as calculated by <code>count_codons()</code>.</dd>
<dt>op</dt>
<dd>a character vector of optimal codons. Can be determined automatically by running
<code>est_optimal_codons</code>.</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>...</dt>
<dd>other arguments passed to <code>est_optimal_codons</code>.</dd></dl>

Arguments

Fraction of optimal codons (Fop) — get_fop

<dl>

<dt>cf</dt>
<dd>matrix of codon frequencies as calculated by <code>count_codons()</code>.</dd>


<dt>op</dt>
<dd>a character vector of optimal codons. Can be determined automatically by running
<code>est_optimal_codons</code>.</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>...</dt>
<dd>other arguments passed to <code>est_optimal_codons</code>.</dd>

</dl>

get_fop: Fraction of optimal codons (Fop)

Description

Usage

Value

Arguments

References

Examples