Calculate fold change

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)

gly_fold_change_(expr_mat, groups)

Arguments

exp

A glyexp::experiment() object.

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. Only applicable to gly_fold_change().

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. Character vectors will be automatically converted to factors. If two groups, the first level is the reference group. If more than two groups, pairwise comparisons will be performed, with levels coming first as reference groups.

Value

A tibble with fold change results containing the following columns:

• variable: Variable name

• log2fc: Log2 fold change (log2(group2_mean / group1_mean)) If more than two groups, two additional columns ref_group and test_group will be added.

Details

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

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