4.7.7 Codon odds ratio

Function

rpf_Odd_Ratio compares codon-associated RPF enrichment between control and treatment sample groups. It builds two-dimensional count tables for codon-level signal, calculates odds-ratio-style statistics, corrects p-values, and summarizes significant codon enrichment or depletion.

Input files

Input	Description
RPF density table	Merged Ribo-seq density table, usually RIBO_merged.txt.
Gene list	Optional transcript or gene list. If not provided, all genes are used.
Control and treatment sample names	Comma-separated sample names. These names must match columns in the merged RPF density table.

Parameters

Parameter	Required	Description
-r	Yes	Input RPF density table in TXT format.
-l	No	Gene name or transcript ID list in TXT format. If omitted, all genes are used.
-o	Yes	Output prefix.
--thread	No	Number of threads used for p-value calculation. Default: 1.
-s	No	Ribosomal site used for odds-ratio calculation. Choices: E, P, A. Default: P.
-f	No	Reading frame used for odds-ratio calculation. Choices: 0, 1, 2, all. Default: all.
-c	Yes	Comma-separated control sample names.
-t	Yes	Comma-separated treatment sample names.
-n	No	Normalize RPF counts to RPM before odds-ratio calculation. Disabled by default.
-z	No	Fill empty codon values with 0.01 * minimal value. Disabled by default.
-m	No	Retain transcripts with more than this minimum number of RPFs. Default: 50.
--fdr	No	Significance column used for filtering. Choices: bhfdr, pvalue. Default: bhfdr.
-v	No	Significance threshold for the selected p-value or FDR column. Default: 0.05.
--tis	No	Number of codons after the translation initiation site to discard. Default: 0.
--tts	No	Number of codons before the translation termination site to discard. Default: 0.
--stop	No	Remove stop codons from the codon-level summary table. Disabled by default.
--scale	No	Scaling method for relative odds-ratio summary values. Choices: zscore, minmax. Default: minmax.

Output files

Output	Description
<prefix>_codon_odd_ratio.txt	Significant codon-level odds-ratio result table after filtering by the selected p-value or FDR threshold.
<prefix>_sum_codon_odd_ratio.txt	Codon-level summary table containing control/treatment counts, proportions, and relative values.
<prefix>_odd_lineplot.pdf / .png	Line plot summarizing significant differential codon counts and proportions.
<prefix>_odd_scatter.pdf / .png	Scatter plot comparing control and treatment codon counts/proportions.

Example

rpf_Odd_Ratio \
    -l ../../../1.reference/norm/gene.norm.txt \
    -r ../05.merge/RIBO_merged.txt \
    -c WT_ribo_YPD1,WT_ribo_YPD2,WT_ribo_YPD3 \
    -t ncs2d_ribo_YPD1,ncs2d_ribo_YPD2,ncs2d_ribo_YPD3 \
    --stop \
    -m 50 \
    -f 0 \
    -s A \
    --tis 10 \
    --tts 5 \
    --fdr bhfdr \
    -v 0.05 \
    -o A_site \
    &> A_site_odd_ratio.log

Notes

• The sample names provided to -c and -t must exactly match sample columns in the merged density table.
• Use --fdr bhfdr for Benjamini-Hochberg FDR filtering or --fdr pvalue for raw p-value filtering.
• The command generates line and scatter plots in the current implementation. The internal barplot function exists but is not called by the command-line workflow.
• Interpret odds-ratio results together with pausing, occupancy, and read-depth information.

Merge related results

Use merge_odd_ratio to merge multiple codon odds-ratio summary tables:

merge_odd_ratio -l *_sum_codon_odd_ratio.txt -o RIBO