Package {REFT}

REFT: Root Exudate Feature Toolkit

Description

REFT is an R package for batch PubChem matching and molecular descriptor calculation from root exudate or metabolomics annotation tables.

Calculate six molecular descriptors

Description

Calculate six descriptors from a character vector of SMILES using rcdk.

Usage

reft_calc_descriptors(smiles)

Arguments

Value

A tibble with six molecular descriptors.

Examples

if (requireNamespace("rcdk", quietly = TRUE)) {
  reft_calc_descriptors("OC(=O)CCC(=O)O")
}

Run KEGG microbe-EC-reaction search workflow

Description

Import a microbial EC annotation table, normalize EC identifiers, extract species names from taxonomy strings, query KEGG for EC-linked reactions, and append reactants, products, and compound formulae. By default, no files are written; set output_dir to explicitly request Excel outputs.

Usage

reft_kegg_microbe_run(
  input_file,
  ec_col = "EC_Number",
  taxonomy_col = "Taxonomy",
  output_dir = NULL,
  output_file = "microbe_ec_kegg_reactions.xlsx",
  sleep_sec = 0.35,
  verbose = TRUE
)

Arguments

Value

A named list containing:

results

Full result table with EC, microbe, reaction, compounds, and formulae.

ec_to_reaction

EC-to-reaction mapping table.

reaction_details

Reaction detail table.

compound_table

Compound formula table.

Examples

toy <- data.frame(
  EC_Number = "1.1.1.1",
  Taxonomy = "k__Bacteria;p__Proteobacteria;g__Escherichia;s__Escherichia_coli"
)
input_file <- tempfile(fileext = ".csv")
utils::write.csv(toy, input_file, row.names = FALSE)
res <- try(
  reft_kegg_microbe_run(input_file, output_dir = tempdir(), sleep_sec = 0,
                        verbose = FALSE),
  silent = TRUE
)
if (!inherits(res, "try-error")) head(res$results)

Match SMILES from PubChem

Description

Batch match SMILES using Name, Other Name, KEGG ID, and HMDB ID in order.

Usage

reft_match_smiles(
  data,
  name_col = "Name",
  other_col = "Other_name(Kegg_name)",
  hmdb_col = "HMDB_ID",
  kegg_col = "Kegg_ID"
)

Arguments

Value

A data frame with matching log and SMILES.

Examples

dat <- data.frame(
  Name = "Glutarate",
  `Other_name(Kegg_name)` = NA,
  HMDB_ID = NA,
  Kegg_ID = NA,
  check.names = FALSE
)
res <- try(reft_match_smiles(dat), silent = TRUE)
if (!inherits(res, "try-error")) head(res)

Run the full REFT workflow

Description

Import an Excel table, clean query fields, match SMILES from PubChem, calculate six molecular descriptors, and optionally write Excel outputs. By default, no files are written; set output_dir to explicitly request Excel outputs.

Usage

reft_run(
  input_file,
  name_col = "Name",
  other_col = "Other_name(Kegg_name)",
  hmdb_col = "HMDB_ID",
  kegg_col = "Kegg_ID",
  output_dir = NULL,
  output_desc_file = "metabolites_6_descriptors.xlsx",
  output_unmatched_file = "unmatched_smiles.xlsx",
  output_log_file = "pubchem_match_log.xlsx",
  verbose = TRUE
)

Arguments

Value

A named list with three data frames:

descriptors

Final annotation table with SMILES and six descriptors.

unmatched

Rows that could not be matched to SMILES.

match_log

Unique-query matching log from PubChem.

Examples

toy <- data.frame(
  Name = "Glutarate",
  `Other_name(Kegg_name)` = NA,
  HMDB_ID = NA,
  Kegg_ID = NA,
  check.names = FALSE
)
if (requireNamespace("rcdk", quietly = TRUE)) {
  input_file <- tempfile(fileext = ".xlsx")
  writexl::write_xlsx(toy, input_file)
  res <- try(reft_run(input_file, output_dir = tempdir(), verbose = FALSE),
             silent = TRUE)
  if (!inherits(res, "try-error")) head(res$descriptors)
}

Run REFT with default column names

Description

A simplified wrapper around reft_run() for the common case where the input file already uses the default column names. By default, no files are written; set output_dir to explicitly request Excel outputs.

Usage

reft_run_simple(input_file, output_dir = NULL, verbose = TRUE)

Arguments

Value

Same as reft_run().

Examples

toy <- data.frame(
  Name = "Glutarate",
  `Other_name(Kegg_name)` = NA,
  HMDB_ID = NA,
  Kegg_ID = NA,
  check.names = FALSE
)
if (requireNamespace("rcdk", quietly = TRUE)) {
  input_file <- tempfile(fileext = ".xlsx")
  writexl::write_xlsx(toy, input_file)
  res <- try(reft_run_simple(input_file, output_dir = tempdir(), verbose = FALSE),
             silent = TRUE)
  if (!inherits(res, "try-error")) head(res$descriptors)
}