Clean up examples and tests

[KarinSchork]

No description provided.

[Copilot]

Pull request overview

This PR updates the package’s examples, vignettes, and test suite to use a new smaller, curated yeast FASTA + filtered MaxQuant peptide table, and refreshes many expectations/snapshots accordingly. It also introduces a script under inst/scripts/ documenting how the new test fixtures were produced.

Changes:

• Switch examples/tests/vignette inputs from legacy uniprot_test.fasta / peptides.txt to uniprot_proteome_Scerevisiae_filtered.fasta / peptides_filtered.txt and new precomputed .rds fixtures.
• Refactor multiple tests to rely on packaged inst/extdata/*.rds objects and update snapshots for the new data.
• Expand/refresh documentation examples across Roxygen + Rd pages to match the new fixtures.

Reviewed changes

Copilot reviewed 58 out of 79 changed files in this pull request and generated 11 comments.

Show a summary per file

File	Description
vignettes/bppg.Rmd	Updates vignette example inputs to new filtered extdata files.
tests/testthat/testfiles/uniprot_proteome_Scerevisiae_filtered.fasta	Adds a FASTA fixture under tests/testthat/testfiles/.
tests/testthat/test-helpers-getProteinOrigin.R	Updates test to use new FASTA extdata and adjusts accession grouping.
tests/testthat/test_wrapperGraph.R	Updates graph-generation tests to use new FASTA and peptide extdata; adjusts expected graph counts.
tests/testthat/test_plotting.R	Minor test cleanup/formatting for snapshot file expectations.
tests/testthat/test_isomorphism.R	Replaces explicit edge-list equality with snapshots.
tests/testthat/test_helpers.R	Changes helper tests to use packaged quantGraphs.rds fixture and snapshot vertex attrs.
tests/testthat/test_graphStatistics.R	Switches graph-statistics tests to packaged .rds fixtures; snapshots updated.
tests/testthat/test_07_resultAggregation_and_Export.R	Uses packaged resultsList.rds instead of constructing results in-test; updates snapshots.
tests/testthat/test_06_optimization.R	Refactors optimization tests to use packaged quantGraphs.rds and snapshot outputs.
tests/testthat/test_05_proteinElimination.R	Switches protein-elimination test to packaged quantGraphs.rds; adjusts numeric tolerance approach.
tests/testthat/test_04_graphGeneration.R	Updates contraction/graph-generation tests to new FASTA + peptide extdata and new .rds fixtures.
tests/testthat/test_03_FASTAPreprocessing.R	Updates FASTA preprocessing tests to new FASTA extdata; minor formatting.
tests/testthat/test_02_peptideProcessing.R	Refactors peptide processing tests to use packaged peptide table; comments out synthetic-data scaffolding.
tests/testthat/test_01_peptideInput.R	Switches peptide input test to packaged peptides_filtered.txt.
tests/testthat/_snaps/isomorphism.md	Adds new snapshot output for isomorphism tests.
tests/testthat/_snaps/helpers.md	Adds new snapshot output for helper tests.
tests/testthat/_snaps/graphStatistics.md	Updates/expands snapshots for graph-statistics outputs under new fixtures.
tests/testthat/_snaps/07_resultAggregation_and_Export.md	Updates aggregation/export snapshots for new comparison naming and fixture outputs.
tests/testthat/_snaps/06_optimization.md	Updates optimization snapshots to match new fixtures and snapshot strategy.
tests/testthat/_snaps/05_proteinElimination.md	Updates protein elimination snapshot outputs to match new fixtures.
R/wrapperGraph.R	Updates examples to new FASTA/peptide extdata; minor formatting.
R/plotting.R	Updates examples to use packaged graphs and removes outdated TODO comments.
R/isomorphism.R	Adds concrete examples for .isomorphicBipartite() and .generatePrototypeList(); improves comments.
R/helpers.R	Updates .addUniquenessAttributes() examples and minor style cleanup.
R/graphStatistics.R	Adds example for .calculateProteinNodeInfo() and minor formatting.
R/07_resultAggregation_and_Export.R	Adds runnable examples for combineComparisons() / exportSE() (but currently using inst/ paths).
R/06_optimization.R	Updates examples to new fixtures and changes filtering logic in automatedAnalysisIteratedCi().
R/05_proteinElimination.R	Expands examples and minor formatting; still references an old removed fixture filename.
R/04_graphGeneration.R	Updates examples and test logic to new fixture inputs; minor formatting.
R/03_FASTAPreprocessing.R	Updates examples and comments; minor formatting.
R/02_peptidePreprocessing.R	Updates examples to new peptide extdata and revised pipeline steps.
R/01_peptideInput.R	Updates examples and modifies decoy/contaminant filtering logic; minor formatting.
man/readMqPeptideTable.Rd	Updates example input file to peptides_filtered.txt.
man/proteinElimination.Rd	Updates example graph indexing but still references old removed fixture filename.
man/plotBipartiteGraph.Rd	Updates example to use packaged quantGraphs_collpept.rds.
man/normalizePeptideIntensities.Rd	Updates example input file to peptides_filtered.txt.
man/iterateOverCi.Rd	Updates example to use quantGraphs.rds and new comparison naming.
man/generateQuantGraphs.Rd	Updates example to new FASTA/peptide extdata and revised preprocessing steps.
man/generateGraphsFromQuantData.Rd	Updates examples and input fixtures to new extdata.
man/generateGraphsFromFASTA.Rd	Updates FASTA example to new extdata.
man/generateGraphsFromEdgelist.Rd	Updates edgelist generation example to new FASTA extdata and collapsing options.
man/exportSE.Rd	Adds runnable example (currently uses inst/ paths in source R).
man/dot-minimizeSquaredError.Rd	Updates example to quantGraphs.rds and new comparison naming.
man/dot-isomorphicBipartite.Rd	Adds explicit example usage.
man/dot-getContractMapping.Rd	Updates example to new FASTA extdata.
man/dot-generatePrototypeList.Rd	Updates argument description and adds explicit example usage.
man/dot-directBipartiteGraph.Rd	Removes placeholder TODO example block.
man/dot-digest2.Rd	Updates example to new FASTA extdata and clarifies intent.
man/dot-contractGraph.Rd	Updates example to new FASTA extdata.
man/dot-calculateSubgraphCharacteristics.Rd	Adds placeholder examples section.
man/dot-calculateProteinNodeInfo.Rd	Adds explicit example usage with quantGraphs.rds.
man/dot-addUniquenessAttributes.Rd	Updates example to use packaged quantGraphs.rds.
man/digestFASTA.Rd	Updates example to new FASTA extdata and fixes a link target.
man/combineComparisons.Rd	Adds examples for combining comparisons (source R currently uses inst/ paths).
man/calculatePeptideRatios.Rd	Updates example to new peptide extdata and revised preprocessing steps.
man/automatedAnalysisIteratedCi.Rd	Updates example to quantGraphs.rds and new comparison naming.
man/aggregateReplicates.Rd	Updates docs/examples to new peptide extdata and revised preprocessing steps.
inst/scripts/filter_fasta_and_quantData.R	Adds script documenting how filtered extdata + .rds fixtures were generated.
inst/extdata/uniprot_test.fasta	Removes legacy test FASTA fixture.
inst/extdata/uniprot_proteome_Scerevisiae_filtered.fasta	Adds new curated FASTA fixture under package extdata.
DESCRIPTION	Updates suggested packages and adds Config/roxygen2/version.

Files not reviewed (5)

• man/aggregateReplicates.Rd: Language not supported
• man/automatedAnalysisIteratedCi.Rd: Language not supported
• man/calculatePeptideRatios.Rd: Language not supported
• man/combineComparisons.Rd: Language not supported
• man/digestFASTA.Rd: Language not supported

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[Copilot]

Pull request overview

Copilot reviewed 57 out of 98 changed files in this pull request and generated 5 comments.

Files not reviewed (5)

• man/aggregateReplicates.Rd: Language not supported
• man/automatedAnalysisIteratedCi.Rd: Language not supported
• man/calculatePeptideRatios.Rd: Language not supported
• man/combineComparisons.Rd: Language not supported
• man/digestFASTA.Rd: Language not supported

[biwenzel]

ne, das muss normalize sein, weil es das assay $intensities_norm erwartet, das gibt es nur nach normalizePeptideIntensities (deswegen ist no norm erlaubt, was dann nur die daten dahin schiebt)