Skip to contents

Two-sample t-test for Differential Expression Analysis

gly_ttest.Rd

Perform two-sample t-test for glycomics or glycoproteomics data. The function supports Student's t-test for comparing two groups. P-values are adjusted for multiple testing using the method specified by p_adj_method.

Usage

gly_ttest(
  exp,
  group_col = "group",
  p_adj_method = "BH",
  ref_group = NULL,
  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.

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::t.test().

Value

A list with three elements:

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

    • variable: Variable name

    • estimate: Difference in group means (group2 - group1)

    • estimate1: Mean of group 1

    • estimate2: Mean of group 2

    • statistic: t-statistic

    • p_val: Raw p-value from t-test

    • parameter: Degrees of freedom

    • conf_low: Lower bound of 95% confidence interval

    • conf_high: Upper bound of 95% confidence interval

    • effect_size: Cohen's d

    • 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))

  • raw_result: A list of t.test model objects

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

Details

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

See also

stats::t.test()