Compare R6 Reference vs. Copy Semantics in Data Filtering
Summary
This skill verifies whether R6-based filter functions in mpactr apply in-place modification (reference semantics with copy_object=FALSE) or create independent copies (deep copy with copy_object=TRUE) by comparing row counts and object identity between the original and assigned result objects. It is essential for understanding memory efficiency and data mutation side effects in metabolomics peak filtering workflows.
When to use
Apply this skill when you need to understand or validate whether calling filter_mispicked_ions() (or similar R6 filter methods) with different copy_object settings will mutate your original data object in memory or preserve it. This is critical before running large-scale filtering on datasets like the cultures peak table (1407 ions initially) to avoid unintended in-place modifications or unnecessary memory duplication.
When NOT to use
- You are not modifying the filtering parameters or workflow—use this skill only if you are varying the copy_object parameter itself.
- Your peak table is already filtered and you are analyzing downstream results (e.g., fold change, volcano plots)—this skill applies only to the filter function call itself.
- You do not have access to reload the same dataset twice or cannot compare two independent filtering runs—the comparison requires fresh imports for each setting.
Inputs
- Raw LC-MS peak table in Progenesis CSV format (e.g., cultures_peak_table.csv)
- Sample metadata in CSV format (e.g., cultures_metadata.csv)
- Imported mpactr data object (R6 instance with peak table and metadata)
Outputs
- Comparison table with rows for each copy_object setting, columns: copy_object, original_object_rowcount, assigned_object_rowcount, object_identity_match
- Validated evidence that copy_object=FALSE causes in-place mutation or copy_object=TRUE creates independent copies
How to apply
Load the same raw LC-MS peak table twice using mpactr::import_data() with format='Progenesis'. On the first copy, call filter_mispicked_ions() with copy_object=FALSE and merge_peaks=TRUE, merge_method='sum'; record the row count of both the original object and the newly assigned result object using get_peak_table(). Reload the data and on the second copy, call filter_mispicked_ions() with identical filtering parameters but copy_object=TRUE; again record row counts. Construct a comparison table with columns: copy_object setting, original_object_rowcount, assigned_object_rowcount, and object_identity_match. If copy_object=FALSE, the original and assigned object should have matching post-filter row counts (indicating in-place mutation); if copy_object=TRUE, they should differ (indicating independent deep copies). This empirical comparison reveals whether the R6 object's reference semantics are actually triggered by the parameter.
Related tools
- mpactr (Provides R6-based filter_mispicked_ions() function with copy_object parameter and get_peak_table() method for extracting row counts) — https://github.com/mums2/mpactr
- R (Language runtime for executing import_data(), filter_mispicked_ions(), and get_peak_table() calls; environment for object identity tracking)
- data.table (Underlying data structure for peak table representation and row count extraction)
Examples
data2 <- import_data(example_path('cultures_peak_table.csv'), format='Progenesis'); data2_filtered_FALSE <- filter_mispicked_ions(data2, merge_peaks=TRUE, merge_method='sum', copy_object=FALSE); nrow1_orig <- nrow(get_peak_table(data2)); nrow1_result <- nrow(get_peak_table(data2_filtered_FALSE)); print(paste('copy_object=FALSE: original=', nrow1_orig, ', result=', nrow1_result, sep=''))
Evaluation signals
- When copy_object=FALSE, original_object_rowcount equals assigned_object_rowcount post-filter (both reflect the filtered state), confirming in-place mutation.
- When copy_object=TRUE, original_object_rowcount remains at pre-filter state while assigned_object_rowcount equals post-filter state, confirming independent deep copy.
- Row count reduction is consistent with the filtering operation (e.g., 1407 → 644 ions for mispicked filter with merge_peaks=TRUE, merge_method='sum').
- No errors or warnings from mpactr::get_peak_table() when extracting counts from both original and assigned objects.
- The comparison table shows one row with copy_object=FALSE and a second row with copy_object=TRUE, demonstrating both settings were tested on identical input data.
Limitations
- This skill requires reloading the same dataset twice, which may be impractical for very large LC-MS datasets or in resource-constrained environments.
- The comparison is specific to filter_mispicked_ions(); other mpactr filters (filter_group, filter_cv, filter_insource_ions) may exhibit different R6 reference semantics behavior and should be validated separately.
- Row count alone does not capture whether nested data structures (e.g., metadata, feature annotations) are also mutated in place; a full object identity check or deep inspection of all slots may be needed for comprehensive validation.
- The copy_object parameter is specific to mpactr R6 filters; this skill does not apply to traditional R functions or copy-by-value workflows.
Evidence
- [other] When filter_mispicked_ions() is called with copy_object=FALSE, the original data object is updated in-place; the raw data object with 7269 ions was reduced to 6625 ions, and the original data2 object was also updated despite assigning the result to a new variable data2_mispicked.: "When filter_mispicked_ions() is called with copy_object=FALSE, the original data object is updated in-place"
- [other] Running filter_mispicked_ions with copy_object=FALSE (the default setting) updates the original data object in place: data2 had 1407 ions before filtering, and after assigning the filtered result to data2_mispicked with copy_object=FALSE, both data2_mispicked and the original data2 contain 644 ions, confirming in-place modification rather than creation of independent copies.: "both data2_mispicked and the original data2 contain 644 ions, confirming in-place modification"
- [abstract] operates on reference semantics in which data is updated in-place. Compared to a shallow copy, where only data pointers are copied, or a deep copy, where the entire data object is copied in memory,: "operates on reference semantics in which data is updated in-place"
- [abstract] Memory usage really shines when you use R6 classes vs. a traditional workflow, such as copy by: "Memory usage really shines when you use R6 classes vs. a traditional workflow"
- [methods] filter_mispicked_ions(merge_peaks = TRUE, merge_method = "sum"): "filter_mispicked_ions(merge_peaks = TRUE, merge_method = "sum")"
- [methods] import_data(example_path("cultures_peak_table.csv"): "import_data(example_path("cultures_peak_table.csv")"
1---2name: r6-reference-semantics-comparison-23description: Use when you need to understand or validate whether calling filter_mispicked_ions() (or similar R6 filter methods) with different copy_object settings will mutate your original data object in memory or preserve it.4license: CC-BY-4.05---67# Compare R6 Reference vs. Copy Semantics in Data Filtering89## Summary1011This skill verifies whether R6-based filter functions in mpactr apply in-place modification (reference semantics with copy_object=FALSE) or create independent copies (deep copy with copy_object=TRUE) by comparing row counts and object identity between the original and assigned result objects. It is essential for understanding memory efficiency and data mutation side effects in metabolomics peak filtering workflows.1213## When to use1415Apply this skill when you need to understand or validate whether calling filter_mispicked_ions() (or similar R6 filter methods) with different copy_object settings will mutate your original data object in memory or preserve it. This is critical before running large-scale filtering on datasets like the cultures peak table (1407 ions initially) to avoid unintended in-place modifications or unnecessary memory duplication.1617## When NOT to use1819- You are not modifying the filtering parameters or workflow—use this skill only if you are varying the copy_object parameter itself.20- Your peak table is already filtered and you are analyzing downstream results (e.g., fold change, volcano plots)—this skill applies only to the filter function call itself.21- You do not have access to reload the same dataset twice or cannot compare two independent filtering runs—the comparison requires fresh imports for each setting.2223## Inputs2425- Raw LC-MS peak table in Progenesis CSV format (e.g., cultures_peak_table.csv)26- Sample metadata in CSV format (e.g., cultures_metadata.csv)27- Imported mpactr data object (R6 instance with peak table and metadata)2829## Outputs3031- Comparison table with rows for each copy_object setting, columns: copy_object, original_object_rowcount, assigned_object_rowcount, object_identity_match32- Validated evidence that copy_object=FALSE causes in-place mutation or copy_object=TRUE creates independent copies3334## How to apply3536Load the same raw LC-MS peak table twice using mpactr::import_data() with format='Progenesis'. On the first copy, call filter_mispicked_ions() with copy_object=FALSE and merge_peaks=TRUE, merge_method='sum'; record the row count of both the original object and the newly assigned result object using get_peak_table(). Reload the data and on the second copy, call filter_mispicked_ions() with identical filtering parameters but copy_object=TRUE; again record row counts. Construct a comparison table with columns: copy_object setting, original_object_rowcount, assigned_object_rowcount, and object_identity_match. If copy_object=FALSE, the original and assigned object should have matching post-filter row counts (indicating in-place mutation); if copy_object=TRUE, they should differ (indicating independent deep copies). This empirical comparison reveals whether the R6 object's reference semantics are actually triggered by the parameter.3738## Related tools3940- **mpactr** (Provides R6-based filter_mispicked_ions() function with copy_object parameter and get_peak_table() method for extracting row counts) — https://github.com/mums2/mpactr41- **R** (Language runtime for executing import_data(), filter_mispicked_ions(), and get_peak_table() calls; environment for object identity tracking)42- **data.table** (Underlying data structure for peak table representation and row count extraction)4344## Examples4546```47data2 <- import_data(example_path('cultures_peak_table.csv'), format='Progenesis'); data2_filtered_FALSE <- filter_mispicked_ions(data2, merge_peaks=TRUE, merge_method='sum', copy_object=FALSE); nrow1_orig <- nrow(get_peak_table(data2)); nrow1_result <- nrow(get_peak_table(data2_filtered_FALSE)); print(paste('copy_object=FALSE: original=', nrow1_orig, ', result=', nrow1_result, sep=''))48```4950## Evaluation signals5152- When copy_object=FALSE, original_object_rowcount equals assigned_object_rowcount post-filter (both reflect the filtered state), confirming in-place mutation.53- When copy_object=TRUE, original_object_rowcount remains at pre-filter state while assigned_object_rowcount equals post-filter state, confirming independent deep copy.54- Row count reduction is consistent with the filtering operation (e.g., 1407 → 644 ions for mispicked filter with merge_peaks=TRUE, merge_method='sum').55- No errors or warnings from mpactr::get_peak_table() when extracting counts from both original and assigned objects.56- The comparison table shows one row with copy_object=FALSE and a second row with copy_object=TRUE, demonstrating both settings were tested on identical input data.5758## Limitations5960- This skill requires reloading the same dataset twice, which may be impractical for very large LC-MS datasets or in resource-constrained environments.61- The comparison is specific to filter_mispicked_ions(); other mpactr filters (filter_group, filter_cv, filter_insource_ions) may exhibit different R6 reference semantics behavior and should be validated separately.62- Row count alone does not capture whether nested data structures (e.g., metadata, feature annotations) are also mutated in place; a full object identity check or deep inspection of all slots may be needed for comprehensive validation.63- The copy_object parameter is specific to mpactr R6 filters; this skill does not apply to traditional R functions or copy-by-value workflows.6465## Evidence6667- [other] When filter_mispicked_ions() is called with copy_object=FALSE, the original data object is updated in-place; the raw data object with 7269 ions was reduced to 6625 ions, and the original data2 object was also updated despite assigning the result to a new variable data2_mispicked.: "When filter_mispicked_ions() is called with copy_object=FALSE, the original data object is updated in-place"68- [other] Running filter_mispicked_ions with copy_object=FALSE (the default setting) updates the original data object in place: data2 had 1407 ions before filtering, and after assigning the filtered result to data2_mispicked with copy_object=FALSE, both data2_mispicked and the original data2 contain 644 ions, confirming in-place modification rather than creation of independent copies.: "both data2_mispicked and the original data2 contain 644 ions, confirming in-place modification"69- [abstract] operates on reference semantics in which data is updated *in-place*. Compared to a shallow copy, where only data pointers are copied, or a deep copy, where the entire data object is copied in memory,: "operates on reference semantics in which data is updated *in-place*"70- [abstract] Memory usage really shines when you use R6 classes vs. a traditional workflow, such as copy by: "Memory usage really shines when you use R6 classes vs. a traditional workflow"71- [methods] filter_mispicked_ions(merge_peaks = TRUE, merge_method = "sum"): "filter_mispicked_ions(merge_peaks = TRUE, merge_method = "sum")"72- [methods] import_data(example_path("cultures_peak_table.csv"): "import_data(example_path("cultures_peak_table.csv")"
HolobiomicsLab 