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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,
  ...
)

gly_ttest_(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_ttest().

...

Additional arguments passed to stats::t.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 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_value: 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

    • 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 The list has classes glystats_ttest_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_ttest() is the top-level API that works with glyexp::experiment() objects and supports the add_info parameter for joining experiment metadata.

gly_ttest_() 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::t.test()