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Calculate fold change

gly_fold_change.Rd

Calculate fold change for a given expression matrix and group information. It could only be used for 2-group analysis. When you run this function, you will see message about "Ref Group" and "Test Group". "Ref Group" is the reference group, and "Test Group" is the test/treatment/case group.

Usage

gly_fold_change(
  exp,
  group_col = "group",
  add_info = TRUE,
  log_transform = FALSE
)

Arguments

exp

A glyexp::GlycomicSE() or glyexp::GlycoproteomicSE() object, or another SummarizedExperiment.

group_col

The column name of the group information in the sample information.

add_info

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

log_transform

A single non-missing logical. If FALSE (default), return the log2 ratio of arithmetic group means as before. If TRUE, apply log2(x + 1e-6) and return the difference of group means on that scale, equivalent to the log2 ratio of geometric means of x + 1e-6. This option transforms input expression; it does not toggle the log2 scale of the reported fold change.

Value

A list with three elements:

  • tidy_result: A tibble with fold change results containing the following columns:

    • variable: Variable name

    • log2fc: Log2 ratio of arithmetic group means by default, or difference of mean log2-transformed values when log_transform = TRUE. If more than two groups, two additional columns ref_group and test_group will be added.

  • raw_result: The raw result (same as tidy_result for this function)

  • meta_data: A list containing metadata from the input experiment