est_csc

<code>get_csc</code> calculate codon occurrence to mRNA stability correlation coefficients (Default to Pearson's).

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_csc function

<dl><dt>seqs</dt>
<dd>CDS sequences of all protein-coding genes. One for each gene.</dd>
<dt>half_life</dt>
<dd>data.frame of mRNA half life (gene_id &amp; half_life are column names).</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>cor_method</dt>
<dd>method name passed to `cor.test` used for calculating correlation coefficients.</dd></dl>

Arguments

Estimate Codon Stabilization Coefficient — est_csc

<dl>

<dt>seqs</dt>
<dd>CDS sequences of all protein-coding genes. One for each gene.</dd>


<dt>half_life</dt>
<dd>data.frame of mRNA half life (gene_id &amp; half_life are column names).</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>cor_method</dt>
<dd>method name passed to `cor.test` used for calculating correlation coefficients.</dd>

</dl>

est_csc: Estimate Codon Stabilization Coefficient

Description

Usage

Value

Arguments

References

Examples