est_optimal_codons

<code>est_optimal_codons</code> determine optimal codon of each codon family with binomial regression.
 Usage of optimal codons should correlate negatively with enc.

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_optimal_codons function

<dl><dt>cf</dt>
<dd>matrix of codon frequencies as calculated by <code>count_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>level</dt>
<dd>"subfam" (default) or "amino_acid". For which level to determine optimal codons.</dd>
<dt>gene_score</dt>
<dd>a numeric vector of scores for genes. The order of values should match with
gene orders in the codon frequency matrix. The length of the vector should be equal to the
number of rows in the matrix. The scores could be gene expression levels (RPKM or TPM) that are
optionally log-transformed (for example, with <code>log1p</code>). The opposite of ENC will be used by
default if <code>gene_score</code> is not provided.</dd>
<dt>fdr</dt>
<dd>false discovery rate used to determine optimal codons.</dd></dl>

Arguments

Estimate optimal codons — est_optimal_codons

<dl>

<dt>cf</dt>
<dd>matrix of codon frequencies as calculated by <code>count_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>level</dt>
<dd>"subfam" (default) or "amino_acid". For which level to determine optimal codons.</dd>


<dt>gene_score</dt>
<dd>a numeric vector of scores for genes. The order of values should match with
gene orders in the codon frequency matrix. The length of the vector should be equal to the
number of rows in the matrix. The scores could be gene expression levels (RPKM or TPM) that are
optionally log-transformed (for example, with <code>log1p</code>). The opposite of ENC will be used by
default if <code>gene_score</code> is not provided.</dd>


<dt>fdr</dt>
<dd>false discovery rate used to determine optimal codons.</dd>

</dl>

est_optimal_codons: Estimate optimal codons

Description

Usage

Value

Arguments

Examples