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

smiles

A character vector of SMILES.

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

input_file	Path to input annotation table.
ec_col	Column containing EC numbers. Default is "EC_Number".
taxonomy_col	Column containing taxonomy strings. Default is "Taxonomy".
output_dir	Output directory. If NULL (default), no files are written.
output_file	Output Excel filename. Default is "microbe_ec_kegg_reactions.xlsx".
sleep_sec	Delay between KEGG requests in seconds. Default is 0.35.
verbose	Whether to print progress. Default is TRUE.

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

data	A data frame containing query columns.
name_col	Compound name column.
other_col	Alternative name column.
hmdb_col	HMDB ID column.
kegg_col	KEGG ID column.

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

input_file	Path to the input Excel file.
name_col	Column name for compound name. Default is "Name".
other_col	Column name for alternative name. Default is "Other_name(Kegg_name)".
hmdb_col	Column name for HMDB identifier. Default is "HMDB_ID".
kegg_col	Column name for KEGG identifier. Default is "Kegg_ID".
output_dir	Output directory. If NULL (default), no files are written.
output_desc_file	Final descriptor Excel filename.
output_unmatched_file	Unmatched records Excel filename.
output_log_file	PubChem match log Excel filename.
verbose	Whether to print progress. Default is TRUE.

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

input_file	Path to the input Excel file.
output_dir	Output directory. If NULL (default), no files are written.
verbose	Whether to print progress. Default is TRUE.

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)
}

---