Hupo changes

[tonywu1999]

User description

Motivation and Context

Got the following error: INDRA Exception: Unexpected number of matches for the following HGNC IDs in the input data: 1578 or 8729

This had to do with how we were filtering on the input. Without those which statements, the table slicing operation creates NA entries.

Changes

Please provide a detailed bullet point list of your changes.

Testing

Please describe any unit tests you added or modified to verify your changes.

Checklist Before Requesting a Review

• I have read the MSstats contributing guidelines
• My changes generate no new warnings
• Any dependent changes have been merged and published in downstream modules
• Ran styler::style_pkg(transformers = styler::tidyverse_style(indent_by = 4))
• Ran devtools::document()

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PR Type

Bug fix, Enhancement

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Description

• Added filtering to remove rows with NA adj.pvalue.

• Replaced direct indexing with which for better error handling.

• Improved robustness in filtering and matching operations.

• Addressed potential issues with unexpected HGNC ID matches.

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Changes walkthrough 📝

	Relevant files
Bug fix	utils_getSubnetworkFromIndra.R Improved filtering and matching in INDRA functions              R/utils_getSubnetworkFromIndra.R Added filtering to exclude rows with NA adj.pvalue. Replaced direct indexing with which for better error handling. Enhanced robustness in filtering and matching logic. +3/-2

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[github-actions]

PR Reviewer Guide 🔍

Here are some key observations to aid the review process:

⏱️ Estimated effort to review: 2 🔵🔵⚪⚪⚪

🧪 No relevant tests

🔒 No security concerns identified

⚡ Recommended focus areas for review Filtering Logic The added filtering logic on line 46 removes rows with NA adj.pvalue. Ensure this change does not unintentionally exclude valid data or introduce edge cases that could affect downstream processing. input <- input[!is.na(input$adj.pvalue),] Matching Logic The replacement of direct indexing with which on lines 70-71 improves error handling but may have performance implications or edge cases. Validate that this change behaves as expected for all input scenarios. matched_rows_source <- input[which(input$HgncId == edge$source_id), ] matched_rows_target <- input[which(input$HgncId == edge$target_id), ]

[github-actions]

PR Code Suggestions ✨

Explore these optional code suggestions:

Category	Suggestion	Score
Possible issue	Add a check for column existence Ensure that the input data frame has the adj.pvalue column before attempting to filter rows based on it to avoid runtime errors when the column is missing. R/utils_getSubnetworkFromIndra.R [46] -input <- input[!is.na(input$adj.pvalue),] +if ("adj.pvalue" %in% colnames(input)) { + input <- input[!is.na(input$adj.pvalue),] +} Suggestion importance[1-10]: 9 Why: The suggestion ensures that the code does not throw an error if the adj.pvalue column is missing in the input data frame. This is a critical improvement for robustness and prevents runtime errors.	9
	Check for column existence before filtering Verify that the HgncId column exists in the input data frame before using it in the which function to prevent potential errors when the column is missing. R/utils_getSubnetworkFromIndra.R [70-71] -matched_rows_source <- input[which(input$HgncId == edge$source_id), ] -matched_rows_target <- input[which(input$HgncId == edge$target_id), ] +if ("HgncId" %in% colnames(input)) { + matched_rows_source <- input[which(input$HgncId == edge$source_id), ] + matched_rows_target <- input[which(input$HgncId == edge$target_id), ] +} else { + stop("INDRA Exception: Missing HgncId column in the input data.") +} Suggestion importance[1-10]: 9 Why: This suggestion adds a necessary check to ensure the HgncId column exists in the input data frame before using it in the which function. This prevents potential runtime errors and improves the reliability of the function.	9

[codecov-commenter]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 86.73%. Comparing base (3a08390) to head (402d447).

Additional details and impacted files

@@            Coverage Diff             @@
##            devel      #29      +/-   ##
==========================================
+ Coverage   86.69%   86.73%   +0.03%     
==========================================
  Files           7        7              
  Lines         406      407       +1     
==========================================
+ Hits          352      353       +1     
  Misses         54       54              

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