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Wilcoxon rank-sum test for Differential Expression Analysis

gly_wilcox.Rd

Perform Wilcoxon rank-sum test (Mann-Whitney U test) for glycomics or glycoproteomics data. The function supports non-parametric comparison of two groups. P-values are adjusted for multiple testing using the method specified by p_adj_method.

Usage

gly_wilcox(
  exp,
  group_col = "group",
  p_adj_method = "BH",
  ref_group = NULL,
  add_info = TRUE,
  ...
)

gly_wilcox_(expr_mat, groups, p_adj_method = "BH", ref_group = NULL, ...)

Arguments

exp

A glyexp::experiment() object containing 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.

ref_group

A character string specifying the reference group. If NULL (default), the first level of the group factor is used as the reference.

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. Only applicable to gly_wilcox().

...

Additional arguments passed to stats::wilcox.test().

expr_mat

A numeric matrix with variables as rows and samples as columns.

groups

A factor or character vector specifying group membership for each sample. Must have exactly 2 levels. Character vectors will be automatically converted to factors.

Value

A list with two elements:

  • tidy_result: A tibble with Wilcoxon test results containing the following columns:

    • variable: Variable name

    • statistic: Wilcoxon test statistic

    • p_val: Raw p-value from Wilcoxon test

    • method: Statistical method used

    • alternative: Alternative hypothesis

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

    • log2fc: Log2 fold change (log2(group2_mean / group1_mean)) Additional columns from experiment metadata may be included if add_info = TRUE.

  • raw_result: A list of wilcox.test model objects The list has classes glystats_wilcox_res and glystats_res.

Details

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

gly_wilcox() is the top-level API that works with glyexp::experiment() objects and supports the add_info parameter for joining experiment metadata.

gly_wilcox_() is the underlying API that works with matrices and factor vectors directly, providing more flexibility for users who don't use the glyexp package.

See also

stats::wilcox.test()