Translate IDs to/from KEGG, PubChem, Chebi, HMDB

Usage

translate_id(
  data,
  metadata_info = c(InputID = "MetaboliteID", grouping_variable = "term"),
  from = "kegg",
  to = c("pubchem", "chebi", "hmdb"),
  summary = FALSE,
  save_table = "csv",
  path = NULL,
  plot = FALSE
)

Arguments

data: dataframe with at least one column with the target (e.g. metabolite), you can add other columns such as source (e.g. term). Must be "long" DF, meaning one ID per row.
metadata_info: Optional: Column name of Target in input_pk. Default = list(InputID="MetaboliteID" , grouping_variable="term")
from: ID type that is present in your data. Choose between "kegg", "pubchem", "chebi", "hmdb". Default = "kegg"
to: One or multiple ID types to which you want to translate your data. Choose between "kegg", "pubchem", "chebi", "hmdb". Default = c("pubchem","chebi","hmdb")
summary: Optional: If TRUE a long summary tables are created. Default = FALSE
save_table: Optional: File types for the analysis results are: "csv", "xlsx", "txt". Default = "csv"
path: Optional: Path to the folder the results should be saved at. Default = NULL

Value

List with at least three DFs: 1) Original data and the new column of translated ids spearated by comma. 2) Mapping information between Original ID to Translated ID. 3) Mapping summary between Original ID to Translated ID.

Examples

KEGG_Pathways <- MetaProViz::metsigdb_kegg()
Res <- MetaProViz::translate_id(data= KEGG_Pathways, metadata_info = c(InputID="MetaboliteID", grouping_variable="term"), from = c("kegg"), to = c("pubchem", "hmdb"))