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One-way ANOVA for Differential Expression Analysis

gly_anova.Rd

Perform one-way ANOVA for glycomics or glycoproteomics data. The function supports parametric comparison of multiple groups. For significant results, Tukey's HSD post-hoc test is automatically performed. P-values are adjusted for multiple testing using the method specified by p_adj_method.

Usage

gly_anova(exp, group_col = "group", p_adj_method = "BH", add_info = TRUE, ...)

Arguments

exp

A glyexp::GlycomicSE() or glyexp::GlycoproteomicSE() object, or another SummarizedExperiment containing an expression matrix and sample information.

group_col

A character string specifying the column name of the grouping variable in the sample information. Default is "group".

p_adj_method

A character string specifying the method to adjust p-values. See p.adjust.methods for available methods. Default is "BH". If NULL, no adjustment is performed.

add_info

A logical value. If TRUE (default), variable information from the experiment will be added to the result tibble. If FALSE, only the statistical results are returned.

...

Additional arguments passed to stats::aov().

Value

A list containing three elements:

  • tidy_result: A list containing:

    • main_test: A tibble with ANOVA results containing the following columns:

      • variable: Variable name

      • term: ANOVA term (usually "groups")

      • df: Degrees of freedom

      • sumsq: Sum of squares

      • meansq: Mean squares

      • statistic: F-statistic

      • p_val: Raw p-value from ANOVA

      • effect_size: Eta-squared

      • p_adj: Adjusted p-value (if p_adj_method is not NULL)

      • post_hoc: Significant group pairs from post-hoc test, in the format of "ref_vs_test".

    • post_hoc_test: A tibble with pairwise comparison results containing the following columns:

      • variable: Variable name

      • ref_group: Reference group

      • test_group: Test/treatment/case group

      • p_val: Raw p-value from Tukey's HSD test

      • p_adj: Adjusted p-value from Tukey's HSD test

  • raw_result: A list containing:

    • main_test: A list of raw aov model objects.

    • post_hoc_test: A list of raw TukeyHSD objects. Post-hoc comparison labels follow the package direction, i.e. test_group - ref_group.

  • meta_data: A list containing metadata from the input experiment.

Details

The function performs log2 transformation on the expression data (log2(x + 1e-6)) before statistical testing. At least 2 groups are required in the grouping variable.

For any variable failed to fit a stats::aov() model, NAs will be assigned to the results in both main test and post-hoc test.

Post-hoc Test: Tukey's HSD test for pairwise comparisons (stats::TukeyHSD()) is performed for variables with significant main effects (p_adj < 0.05).

See also

stats::aov(), stats::TukeyHSD()