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…_per_million - Introduced a new `filterByExpr` function with S3 methods for `DGEList` and `default`. - Updated existing methods to include `minimum_count_per_million` parameter, allowing users to specify a CPM cutoff for filtering. - Adjusted `identify_abundant` and `keep_abundant` methods to accommodate the new parameter, ensuring it overrides `minimum_counts` when provided. - Added tests to validate the functionality of the new filtering options.
…s to include minimum_count_per_million parameter
…ethods - Introduced formula_design parameter to allow users to specify a formula for constructing the design matrix from colData, overriding the design argument if both are provided. - Updated relevant methods to incorporate this new parameter. - Added tests to ensure functionality with the formula_design argument and validate its precedence over the design argument.
…ance handling - Updated identify_abundant and related methods to handle .abundance as a quosure, simplifying the logic for determining the assay name. - Removed unnecessary debug statements and streamlined the code for clarity. - Ensured compatibility with the existing formula_design parameter, maintaining functionality for users specifying design matrices. - Enhanced overall code readability and maintainability.
…n `methods_SE.R`, `methods.R`, and their corresponding documentation files. This change streamlines the function signatures, focusing on the `.abundance` parameter for clarity and consistency.
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
…arity and performance, including adjustments to handling of data transformations and error checks. Remove deprecated test files to streamline the testing process.
- Updated various methods to replace the deprecated `.abundance` parameter with a new `abundance` character argument for improved clarity and consistency. - Enhanced documentation to reflect these changes and ensure backward compatibility. - Removed unnecessary code related to deprecated parameters, streamlining function signatures and improving overall readability. - Adjusted tests to align with the new parameter structure, ensuring continued functionality and validation of methods.
…ted methods - Introduced `abundance` character argument in place of the deprecated `.abundance` parameter across multiple functions, improving clarity and consistency. - Updated deprecation warnings for `.abundance` to guide users towards the new `abundance` argument. - Added `factor_of_interest` parameter to `identify_abundant` and `keep_abundant` methods, with appropriate deprecation notices for backward compatibility. - Enhanced documentation to reflect these changes and ensure users are informed of deprecated parameters. - Adjusted tests to validate the new parameter structure and ensure continued functionality.
…in `utilities.R` and `validation.R`. This change streamlines the codebase by eliminating unused functions and improving overall readability.
- Introduced a new internal error function `my_stop` for improved error messaging in `utilities.R`. - Removed duplicate `my_stop` function definitions from `get_transcript` and `get_elements_features_abundance` methods, streamlining the code. - Enhanced documentation for the new error function to clarify its purpose and usage. - Deleted the `dplyr-master-methods.R` file, which contained deprecated methods, to clean up the codebase.
- Introduced new test files for abundance normalization, cellularity analysis, clustering, data transformation, differential analysis, dimensionality reduction, filtering and selection, gene enrichment, setup, utility functions, and validation utilities. - Each test file includes multiple test cases to validate the functionality of respective functions, ensuring robustness and reliability. - Implemented skip conditions for tests that require additional packages or have known compatibility issues, maintaining test integrity while acknowledging limitations. - Enhanced overall test coverage for the analysis pipeline, facilitating easier debugging and future development.
- Added new dependencies: `enrichplot`, `patchwork`, and `immunedeconv` to the DESCRIPTION file. - Updated the NAMESPACE to include new imports and removed deprecated functions. - Enhanced README with a new abstract and improved structure, including a bibliography section. - Added comprehensive tests for various functions, ensuring robust coverage for data transformation, normalization, filtering, and analysis methods. - Introduced new figures and vignettes to illustrate functionality and usage of the package. - Removed deprecated `test_differential_cellularity` function and its associated documentation.
…ackages` function to streamline error handling.
- Changed `panel.grid.major` and `panel.grid.minor` to use `linewidth` instead of `size` for better compatibility with ggplot2 updates. - Set `eval=FALSE` for installation code chunks in the Bioconductor and GitHub sections to prevent automatic execution during rendering.
…te documentation - Eliminated the `action` parameter from functions including `adjust_abundance`, `cluster_elements`, `deconvolve_cellularity`, `quantile_normalise_abundance`, `reduce_dimensions`, `rotate_dimensions`, `scale_abundance`, and `test_differential_abundance`. - Updated associated documentation to reflect the removal of the `action` parameter, enhancing clarity and consistency across methods. - Ensured that deprecated parameters are properly noted in the documentation to guide users.
…lyr pipes for improved readability and maintainability. Updated multiple methods including `deconvolve_cellularity`, `describe_transcript`, `get_bibliography`, `rotate_dimensions`, and others to enhance clarity in data manipulation. Additionally, adjusted test cases to reflect changes in function outputs and ensure consistency across the codebase.
- Added `test_differential_expression` as an alias for `test_differential_abundance`, allowing for consistent usage across methods. - Updated the `.gitignore` to exclude `tidybulk.Rcheck/*`. - Enhanced documentation for `test_differential_expression` and adjusted references in vignettes to reflect the new function name. - Refactored internal logic in `test_differential_abundance` for clarity and improved handling of fit objects. - Ensured consistency in parameter naming and descriptions across documentation to enhance user understanding.
- Updated `get_bibliography`, `impute_missing_abundance`, `reduce_dimensions`, and other functions to access and manipulate metadata for improved clarity and consistency. - Enhanced documentation to reflect changes in how methods are accessed, ensuring backward compatibility with internals. - Introduced new utility functions for managing metadata, including `reattach_metadata` and `attach_to_metadata`, to streamline data handling in `SummarizedExperiment` objects.
- Modified `my_CIBERSORT`, `glmmSeq`, and `test_gene_enrichment` functions to set the `cores` parameter to `parallel::detectCores()`, allowing for automatic detection of available CPU cores. - This change enhances performance and flexibility in parallel processing across these functions.
…s and clarity - Updated `test_gene_enrichment` to utilize `roast` method exclusively for enhanced reliability in results. - Modified core functions to dynamically detect available CPU cores using `parallel::detectCores()`, improving performance. - Adjusted test cases to access metadata instead of internals, ensuring consistency and clarity in data handling. - Revised vignettes to reflect changes in function usage and parameters, enhancing user guidance and documentation accuracy.
…U cores during execution. - Adjusted test cases for `deconvolve_cellularity` to include the `cores` parameter, ensuring consistency in testing parallel execution. - Deprecated the `test_stratification_cellularity` function due to formula compatibility issues, with a note for future reference.
…ation_cellularity - Updated the `as_SummarizedExperiment` function to include explicit parameters for `.sample`, `.transcript`, and `.abundance`, improving clarity in usage. - Deprecated the `test_stratification_cellularity` function, updating documentation to reflect its removal in future versions and providing a deprecation warning. - Adjusted related documentation and examples to ensure consistency and clarity across the codebase.
- Added `inner_join` import to NAMESPACE for improved functionality. - Cleaned up documentation in `remove_redundancy` and `rotate_dimensions` functions for better clarity. - Removed unnecessary whitespace in `test_gene_overrepresentation` and adjusted documentation formatting in `rotate_dimensions` methods for consistency.
…erator for improved readability and consistency across the codebase. - Removed the now-unnecessary `utils-pipe.R` file and its associated documentation. - Cleaned up comments and documentation in various functions, including `remove_redundancy`, `rotate_dimensions`, and `test_gene_enrichment`, to enhance clarity and maintainability. - Updated the `NAMESPACE` to reflect the removal of the pipe operator export.
- Replaced instances of the `%>%` pipe operator with the native `|>` operator in `deconvolve_cellularity` and `describe_transcript` functions for improved readability. - Removed the import statement for the `%>%` operator in `get_bibliography` as it is no longer needed.
- Removed the `immunedeconv` dependency from DESCRIPTION as it is no longer needed. - Added a session information code chunk to the conclusion of the `comparison_coding.Rmd` vignette for better reproducibility and context.
- Updated existing figures to reflect recent changes. - Added new figures for differential expression analysis using DESeq2 and edgeR. - Included additional visualizations for EDA and GSEA plots to enhance documentation.
…a/tidybulk into improve-keep_abundant
Add filterByExpr function and update methods to support minimum_count…
…ettes - Deleted the `new_SE_usage-01.png` image as it is no longer needed. - Updated the differential expression testing method in `comparison_coding.Rmd` to use "edgeR_quasi_likelihood" for improved accuracy. - Adjusted contrast specification in `comparison_coding.Rmd` to align with the new method.
- Introduced a new parameter, feature_column, allowing users to specify a column in rowData for feature names instead of using rownames. - Updated documentation to reflect this change and provide usage examples. - Added tests to ensure correct functionality and error handling for feature_column input.
- Improved logic to detect numeric columns in the aggregate_duplicates function, ensuring they are preserved during aggregation. - Added a new test to verify that numeric columns remain numeric and character columns remain character after aggregation. - Ensured the merged_transcripts column is correctly typed as integer.
- Changed references from `se_mini` to `airway` throughout the README and vignettes to standardize the dataset used for examples. - Enhanced the introduction and data overview sections to provide context on the `airway` dataset and its relevance to the analysis. - Updated code snippets to reflect the new dataset, including data loading, preprocessing, and visualization steps. - Removed deprecated `.deconvolve_cellularity_se` documentation and adjusted cellularity analysis examples accordingly. - Updated figures in the README_files to ensure they align with the new content and examples.
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