Skip to contents

Wilcoxon Test for Differential Expression Analysis

gly_wilcox.Rd

Perform Wilcoxon rank-sum or signed-rank tests for glycomics or glycoproteomics data. 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,
  ...,
  subject_col = NULL,
  log_transform = 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.

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.

...

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

subject_col

An optional character string naming the subject identifier column in sample information. When supplied, samples are matched by subject and a paired Wilcoxon signed-rank test is performed.

log_transform

A single non-missing logical value. If TRUE (default), transform expression values using log2(x + 1e-6) before analysis. If FALSE, use the supplied values unchanged, for example for already log-transformed data.

Value

A list with three 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

    • effect_size: Rank-biserial correlation, using matched pairs in paired analyses

    • 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

  • meta_data: A list containing metadata from the input experiment The list has classes glystats_wilcox_res and glystats_res.

Details

Tests and effect sizes use the selected analysis scale. Reported fold changes continue to use ratios of group means from the original supplied values.

By default, expression data are transformed using log2(x + 1e-6) before statistical testing. Set log_transform = FALSE to skip this transformation. Exactly 2 groups are required in the grouping variable. In paired analyses, only subjects observed in both groups are used and effect_size is the matched-pairs rank-biserial correlation.

See also

stats::wilcox.test()