Prepare libraries of retention times

Description

This function prepares retention time libraries by combining experimental and in silico predicted retention times from multiple sources (MGF files, CSV files). It standardizes retention time units, validates structures, and creates both RT libraries and pseudo structure-organism pairs for RT-based annotation.

Usage

prepare_libraries_rt(
  mgf_exp = get_params(step = "prepare_libraries_rt")\$files\$libraries\$temporal\$exp\$mgf,
  mgf_is = get_params(step = "prepare_libraries_rt")\$files\$libraries\$temporal\$is\$mgf,
  temp_exp = get_params(step = "prepare_libraries_rt")\$files\$libraries\$temporal\$exp\$csv,
  temp_is = get_params(step = "prepare_libraries_rt")\$files\$libraries\$temporal\$is\$csv,
  output_rt = get_params(step = "prepare_libraries_rt")\$files\$libraries\$temporal\$prepared,
  output_sop = get_params(step = "prepare_libraries_rt")\$files\$libraries\$sop\$prepared\$rt,
  col_ik = get_params(step = "prepare_libraries_rt")\$names\$mgf\$inchikey,
  col_na = get_params(step = "prepare_libraries_rt")\$names\$mgf\$name,
  col_rt = get_params(step = "prepare_libraries_rt")\$names\$mgf\$retention_time,
  col_sm = get_params(step = "prepare_libraries_rt")\$names\$mgf\$smiles,
  name_inchikey = get_params(step = "prepare_libraries_rt")\$names\$inchikey,
  name_name = get_params(step = "prepare_libraries_rt")\$names\$compound_name,
  name_rt = get_params(step = "prepare_libraries_rt")\$names\$rt\$library,
  name_smiles = get_params(step = "prepare_libraries_rt")\$names\$smiles,
  unit_rt = get_params(step = "prepare_libraries_rt")\$units\$rt
)

Arguments

mgf_exp	character Character vector of paths to MGF files with experimental RT
mgf_is	character Character vector of paths to MGF files with in silico predicted RT
temp_exp	character Character vector of paths to CSV files with experimental RT
temp_is	character Character vector of paths to CSV files with in silico predicted RT
output_rt	character Character string path for prepared RT library output
output_sop	character Character string path for pseudo SOP output
col_ik	character Character string name of InChIKey column in MGF
col_na	character Character string name of chompound name column in MGF
col_rt	character Character string name of retention time column in MGF
col_sm	character Character string name of SMILES column in MGF
name_inchikey	character Character string name of InChIKey column in CSV
name_name	character Character string name of compound name column in CSV
name_rt	character Character string name of retention time column in CSV
name_smiles	character Character string name of SMILES column in CSV
unit_rt	character Character string RT unit: "seconds" or "minutes"

Value

Character string path to the prepared retention time library

See Also

Other preparation: prepare_annotations_gnps(), prepare_annotations_mzmine(), prepare_annotations_sirius(), prepare_annotations_spectra(), prepare_features_components(), prepare_features_edges(), prepare_features_tables(), prepare_libraries_sop_bigg(), prepare_libraries_sop_closed(), prepare_libraries_sop_ecmdb(), prepare_libraries_sop_hmdb(), prepare_libraries_sop_lotus(), prepare_libraries_sop_merged(), prepare_libraries_spectra(), prepare_params(), prepare_taxa()

Examples

library("tima")

copy_backbone()
go_to_cache()
prepare_libraries_rt()
unlink("data", recursive = TRUE)