Gdr 3186

[bczech]

Description

What changed?

Related JIRA issue: GDR-3186

Why was it changed?

To add support for merging additional variables

Checklist for sustainable code base

• I added tests for any code changed/added
• I added documentation for any code changed/added
• I made sure naming of any new functions is self-explanatory and consistent

Logistic checklist

• Package version bumped
• Changelog updated

Screenshots (optional)

[gemini-code-assist]

Summary of Changes

Hello @bczech, I'm Gemini Code Assist¹! I'm currently reviewing this pull request and will post my feedback shortly. In the meantime, here's a summary to help you and other reviewers quickly get up to speed!

This pull request enhances the gDRutils package by adding a significant feature that allows users to merge supplementary metadata variables directly into drug identifier columns during the conversion of SummarizedExperiment and MultiAssayExperiment objects to data.tables. This provides a more enriched and context-aware representation of drug data, improving downstream analysis and reporting by embedding relevant details alongside drug names.

Highlights

• New Feature: Merging Additional Variables: Introduced the capability to merge additional metadata variables into drug identifier columns within the convert_se_assay_to_dt and convert_mae_assay_to_dt functions.
• New Function: update_drug_name: Added a new internal function update_drug_name to facilitate the concatenation of specified additional variables into existing drug identifier columns (e.g., DrugName, Gnumber).
• Enhanced Data Conversion Functions: The convert_se_assay_to_dt and convert_mae_assay_to_dt functions now accept a new boolean parameter merge_additional_variables to control this new merging behavior.
• Package Version Update: The gDRutils package version has been bumped from 1.9.2 to 1.9.3, reflecting the new functionality.
• Comprehensive Testing: New test cases have been added to validate the functionality of update_drug_name and the merge_additional_variables parameter in convert_se_assay_to_dt.

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[gemini-code-assist]

Code Review

This pull request adds functionality to merge additional variables into drug names. The implementation is mostly correct, but I've found a few issues. There are several non-breaking space characters in documentation and comments that should be removed. More critically, a non-breaking space in a formula string could cause a bug. I've also suggested a refactoring for the new update_drug_name function to improve its performance and readability.

[gladkia]

GJ!