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t_table_metactivity_input_formater

Source: R/limma_aux_functions.R
t_table_metactivity_input_formater.Rd

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