4.8.4 smORF integrate

Function

smorf_integrate integrates the long-format ORF-by-sample evidence table generated by smorf_evidence.

It can create an ORF-by-sample matrix for frame-density/evidence metrics and an integrated ORF-level evidence table that summarizes sample support, best evidence labels, RPF metrics, and multi-sample status.

Input files

Input	Required	Description
Evidence table	Yes	Long-format table generated by smorf_evidence. The table must contain at least sample and orf_id columns.

Parameters

Parameter	Required	Description
-i, --input	Yes	Long-format smORF Ribo-seq evidence table generated by smorf_evidence.
-m, --output-matrix	Yes	Output ORF-by-sample matrix table. At least one of --output-matrix or --output-integrated must be provided.
-o, --output-integrated	Yes	Output integrated ORF-level evidence table. At least one of --output-matrix or --output-integrated must be provided.
-c, --capture-labels	No	Translation evidence labels used to define captured samples. Default: LowConfidence,MediumConfidence,HighConfidence.
-p, --pass-labels	No	Translation evidence labels used to define reliable samples. Default: MediumConfidence,HighConfidence.
-n, --excellent-min-samples	No	Minimum number of reliable samples required to mark an ORF as Excellent. Default: 2.

Output files

The command writes one or both of the following files, depending on the selected options:

Output	Description
--output-matrix	ORF-by-sample matrix containing static ORF annotation and sample-specific metrics such as RPF sum, frame density, frame ratio, coverage ratio, and translation evidence.
--output-integrated	Integrated ORF-level evidence table summarizing multi-sample support, summed/max/min metrics, best labels, best sample, and multi-sample status.

Examples

Generate both matrix and integrated evidence table

smorf_integrate \
  -i smorf.riboseq_evidence.txt \
  -m smorf.frame_density_matrix.txt \
  -o smorf.integrated_evidence.txt

Require at least 5 reliable samples for Excellent support

smorf_integrate \
  -i smorf.riboseq_evidence.txt \
  -o smorf.integrated_evidence.txt \
  -p MediumConfidence,HighConfidence \
  -n 5

Notes

• At least one of --output-matrix or --output-integrated must be provided.
• --capture-labels controls which samples are counted as captured or supported.
• --pass-labels controls which samples are counted as reliable support.
• The integrated table adds multi_sample_status, which can be Excellent, SingleSample, CapturedButWeak, or NoEvidence depending on sample support.
• The matrix table is useful for downstream visualization, clustering, or manual inspection across samples.