prepare_libraries_rt

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 vector of paths to MGF files with experimental RT

mgf_is Character vector of paths to MGF files with in silico predicted RT

temp_exp Character vector of paths to CSV files with experimental RT

temp_is Character vector of paths to CSV files with in silico predicted RT

output_rt Character string path for prepared RT library output

output_sop Character string path for pseudo SOP output

col_ik Character string name of InChIKey column in MGF

col_na Character string name of chompound name column in MGF

col_rt Character string name of retention time column in MGF

col_sm Character string name of SMILES column in MGF

name_inchikey Character string name of InChIKey column in CSV

name_name Character string name of compound name column in CSV

name_rt Character string name of retention time column in CSV

name_smiles Character string name of SMILES column in CSV

unit_rt Character string RT unit: "seconds" or "minutes"

Value

Character string path to the prepared retention time library

Examples

library("tima")

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