est_rscu

<code>est_rscu</code> returns the RSCU value of codons

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_rscu function

<dl><dt>cf</dt>
<dd>matrix of codon frequencies as calculated by <code>count_codons()</code>.</dd>
<dt>weight</dt>
<dd>a vector of the same length as <code>seqs</code> that gives different weights
to CDSs when count codons. for example, it could be gene expression levels.</dd>
<dt>pseudo_cnt</dt>
<dd>pseudo count to avoid dividing by zero. This may occur when
only a few sequences are available for RSCU calculation.</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 RSCU.</dd></dl>

Arguments

Estimate RSCU — est_rscu

<dl>

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


<dt>weight</dt>
<dd>a vector of the same length as <code>seqs</code> that gives different weights
to CDSs when count codons. for example, it could be gene expression levels.</dd>


<dt>pseudo_cnt</dt>
<dd>pseudo count to avoid dividing by zero. This may occur when
only a few sequences are available for RSCU calculation.</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 RSCU.</dd>

</dl>

est_rscu: Estimate RSCU

Description

Usage

Value

Arguments

References

Examples