t_table_metactivity_input_formater: t_table_metactivity_input_formater

In saezlab/ocean: metabolic enzyme enrichment analysis

t_table_metactivity_input_formater

Description

This function allows to format a table of t-values (or log2FCs) for the metactivity function. Essentially, it adds a compartment code (using BIGG nomenclature) at the end of each metabolite identifier, so that they can be mapped on the compartmentalized reaction prior knowledge network.

Usage

t_table_metactivity_input_formater(
  metabolomic_t_table,
  mapping_table,
  affixes = c("c", "l", "x", "m", "e", "n", "r")
)

Arguments

metabolomic_t_table	the metabolomic t-table (or log2FC table) that is returned by ttop_list_to_t_table (or ttop_list_to_log2FC_table)
mapping_table	a mapping table to translate the metabolite identifiers of the t-table into KEGG IDs
affixes	a character vectors corresponding to the compartment affixes to be considered. If you wish to only focus on one compartment, e.g. mitochondria, you can input only c("m") for example.

Value

a formatted t-table (or log2FC table) for use with the metactivity function

saezlab/ocean documentation built on Nov. 12, 2024, 5 a.m.