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Address lint violations from updated gDRstyle rules: - Fix trailing whitespace and blank lines - Replace nrow/ncol with NROW/NCOL - Fix paste_linter (paste0+collapse, toString, strrep, file.path) - Fix seq_linter (seq_along, seq_len) - Refactor cyclocomp_linter violations (extract helper functions) - Fix test linters (yoda, expect_true_false) - Remove undesirable operators (|> pipes)
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Code Review
This pull request primarily performs whitespace cleanup across multiple files, including R/data.R, R/import_data.R, and the package vignette. Reviewers identified several typographical and grammatical errors in the documentation, such as typos in data type names and incorrect hyphenation, which represent opportunities for improvement.
| #' Small data.table with raw combo data used for processing via gDR | ||
| #' | ||
| #' A dataset containing the ReadoutValues for combo experiments made-up of | ||
| #' A dataset containing the ReadoutValues for combo experiments made-up of |
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The phrase 'made-up of' should be 'made up of' when used as a verb phrase. 'Made-up' with a hyphen is typically an adjective.
#' A dataset containing the ReadoutValues for combo experiments made up of|
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| ## runDrugResponseProcessingPipeline | ||
| Steps (2) and (3) can be combined into a single step through a convenience function: `runDrugResponseProcessingPipeline`. Moreover, the output is `MultiAssayExperiment` object with one experiment per each detected data type. Currently four data types are supported: 'single-agent', 'cotreatment', 'codilution' and 'matrix'. The first three data types are processed via the 'single-agent' model while the 'marix' data is processed via the 'combintation' model. | ||
| Steps (2) and (3) can be combined into a single step through a convenience function: `runDrugResponseProcessingPipeline`. Moreover, the output is `MultiAssayExperiment` object with one experiment per each detected data type. Currently four data types are supported: 'single-agent', 'cotreatment', 'codilution' and 'matrix'. The first three data types are processed via the 'single-agent' model while the 'marix' data is processed via the 'combintation' model. |
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This line contains typos: 'marix' should be 'matrix' and 'combintation' should be 'combination'. Additionally, consider adding the article 'a' before 'MultiAssayExperiment' for better grammatical flow. Corrected text: Steps (2) and (3) can be combined into a single step through a convenience function: runDrugResponseProcessingPipeline. Moreover, the output is a MultiAssayExperiment object with one experiment per each detected data type. Currently four data types are supported: 'single-agent', 'cotreatment', 'codilution' and 'matrix'. The first three data types are processed via the 'single-agent' model while the 'matrix' data is processed via the 'combination' model.
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Description
What changed?
Related JIRA issue: GDR-1014
Why was it changed?
Updated gDRstyle linting rules require compliance across all gDR packages.
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