Changelog

glystats 0.5.3

Minor improvements and fixes

• glystats now depends on the CRAN version of glyrepr.

glystats 0.5.2

Minor improvements and bug fixes

• Fix the bug in many functions that some parameters cannot be passed by ... to the underlying statistical functions.

glystats 0.5.1

Minor improvements and bug fixes

• Fix bugs introduced by the breaking changes in glyexp 0.10.0.

glystats 0.5.0

This is a big update! We make some breaking changes to the API, mainly DEA functions. Now you can ensure these properties for all DEA results:

• The levels in the front are the reference group. For example, for groups with levels c(“A”, “B”), “A” is the reference group. For groups with levels c(“A”, “B”, “C”), “A” is the reference group in A-B and A-C comparisons, and “B” is the reference group in B-C comparisons.
• For the concept of “comparison”, either in result columns or as arguments, it is expected to be in the format of “ref_vs_test”.

Breaking changes

• The post_hoc column in tidy_result$main_test of results from gly_anova() and gly_kruskal() is now in the format of “ref_vs_test” instead of “ref-test”.
• The group1 and group2 columns in tidy_result$post_hoc_test of results from gly_anova() and gly_kruskal() are renamed into ref_group and test_group for more clarity.
• In the tidy_result of gly_limma(), the comparison column is replaced by the ref_group and test_group columns.
• The results of all functions now have a p_val column for raw p-values, a p_adj column for adjusted p-values, and a log2fc column for log2 fold change, if applicable. This consistence in column naming reduces the cognitive load.

New features

• Add get_tidy_result() and get_raw_result() to get the tidy result tibble and the raw result list from a glystats result object. These functions are useful to be used in pipes.
• Add filter_sig_vars() to filter the experiment using the results from glystats DEA functions to keep only significant variables.
• gly_fold_change() now supports multiple groups.
• The post-hoc results from gly_anova() and gly_kruskal() now have a log2fc column for log2 fold change.

Minor improvements and bug fixes

• Update group information message in many functions. Instead of “Group 1” and “Group 2”, now we use “Ref Group” and “Test Group” for more clarity.
• There are ref_group and test_group columns in the tidy_result tibble of gly_limma() even for 2 groups now.
• Fix the bug that gly_kruskal() failed to work with experiments with 2 groups.
• Fix the bug that the direction of fold change is not consistent when with 2 groups and with multiple groups.
• Fix the bug that gly_anova() and gly_kruskal() have NAs in the post_hoc_test tibble.
• Add glyrepr to dependencies to fix the result printing bug.

glystats 0.4.2

Minor improvements and bug fixes

• Update dependencies to depend on release versions of glycoverse packages.

glystats 0.4.1

Minor improvements and bug fixes

• Fix the could not find function "%||%" bug in gly_anova().
• gly_anova(), gly_kruskal(), gly_ttest(), gly_wilcox(), gly_cox(), gly_roc(), and their gly_xxx_() counterparts are now more robust. Previously, if the model failed to be fitted for any variable, the functions stopped with an error. Now, they only issue a warning and continue, assigning NAs in the results for those failed variables.

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.