Changelog

glystats 0.4.0

Breaking changes

• gly_plsda() now uses the ropls package as its backend instead of mixOmics. This changes the class of the object returned in the raw_result list element, which may affect downstream code that uses the raw result directly.

New features

• Added permutation testing to gly_oplsda() via the new perm_test parameter to assess model significance.
• The result from gly_oplsda() now includes a pcorr column containing p-values for the correlation coefficients of features with the predictive component.

Minor improvements and bug fixes

• Removed the check for n/p in gly_oplsda() and gly_plsda(), increasing flexibility for smaller datasets.
• Improved the error message when a specified grouping column is not found in the sample information.
• Fixed a bug in gly_limma() that could cause duplicated messages to be printed.
• Fixed a bug in gly_oplsda() where the column for the first orthogonal component score (o1) could be missing from the result.
• Suppressed messages from dependency packages and extra blank lines when running gly_enrich_go() for a cleaner console output.
• Removed redundant glystats S3 classes from the tibbles in the tidy_result, simplifying the output object structure.

glystats 0.3.0

Breaking changes

This version introduces new API for all functions. Briefly, the return_raw parameter is removed, and all functions now return a list with two elements: tidy_result and raw_result. The concrete types of tidy_result and raw_result depend. tidy_result can be a tibble, or a list of tibbles. raw_result can be a single object returned by the underlying statistical functions, or a list of such objects. This update makes glystats easier to use. And more importantly, it allows the glyvis package to access the raw results directly.

Minor improvements and bug fixes

• Update the documentation of all functions to include the detailed column descriptions for the tibbles in tidy_result.
• All gly_xxx_() functions now accept a character vector as the groups parameter.
• Fix an issue that gly_consensus_clustering() sends plots to the plot panel when output_file is NULL. This is an inconsistent behavior compared to other functions, and it has been fixed.
• Update the documentation of gly_consensus_clustering() to emphasize the importance of output_file.
• Add an introduction vignette.

glystats 0.2.3

Minor improvements and bug fixes

• Make the parameters of gly_umap() and gly_umap_() consistent.
• Fix a bug that some functions returned values with duplicated S3 classes.
• Fix inconsistent behaviours between gly_tsne() and gly_tsne_().

glystats 0.2.2

Bug fixes

• Fix a bug in test.

glystats 0.2.1

Minor improvements

• Change S3 class of the results of gly_anova(), gly_kruskal(), gly_limma(), gly_ttest(), and gly_wilcox().

glystats 0.2.0

Breaking changes

• gly_anova() and gly_kruskal() now return lists of two tibbles, one for main test and the other for post-hoc test.
• Remove the method, dist_method parameters from gly_hclust().
• Remove the max_iter, theta parameters from gly_tsne().
• Remove the n_epochs, learning_rate, metric parameters from gly_umap().

New features

• Add a new set of API functions: all gly_xxx() functions now have a lower API counterpart gly_xxx_() that works with matrices directly, providing more flexibility for users who don’t use the glyexp package.
• Add gly_limma() and gly_limma_() to perform differential analysis using the limma package.
• Add gly_kmeans() and gly_kmeans_() to perform K-means clustering.
• Add gly_wgcna() and gly_wgcna_() to perform WGCNA analysis.
• Add gly_consensus_clustering() and gly_consensus_clustering_() to perform consensus clustering.
• Add gly_cox() and gly_cox_() to fit Cox proportional hazards model for survival analysis.
• Add ref_group parameter to gly_ttext() and gly_wilcox().

Minor improvements and bug fixes

• Fix the bugs in many functions that parameter validations were not performed.
• Reduce size of the test data.
• Remove dependency on the parameters package.