omu (version 1.1.2)

ra_table: Creates a ratio table from the count_fold_changes function output.

Description

Create a ratio table

Usage

ra_table(fc_data, variable)

Arguments

fc_data

data frame output from the count_fold_changes function

variable

metadata from count_fold_changes, i.e. "Class"

Examples

c57_nos2KO_mouse_countDF <- assign_hierarchy(c57_nos2KO_mouse_countDF, TRUE, "KEGG")
c57_nos2KO_mouse_countDF <- c57_nos2KO_mouse_countDF[1:20,]
t_test_df <- omu_summary(count_data = c57_nos2KO_mouse_countDF,
metadata = c57_nos2KO_mouse_metadata, numerator = "Strep", denominator = "Mock",
response_variable = "Metabolite", Factor = "Treatment",
log_transform = TRUE, p_adjust = "BH", test_type = "welch")

fold_change_counts <- count_fold_changes(count_data = t_test_df,
column = "Class", sig_threshold = 0.05, keep_unknowns = FALSE)

ra_table(fc_data = fold_change_counts, variable = "Class")