prepare_libraries_rt: Prepare libraries of retention times

In taxonomicallyinformedannotation/tima-r: Taxonomically Informed Metabolite Annotation

Prepare libraries of retention times

Description

This function prepares retention times libraries to be used for later

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_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_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	MGF containing experimental retention times
mgf_is	MGF containing in silico predicted retention times
temp_exp	File containing experimental retention times
temp_is	File containing in silico predicted retention times
output_rt	Output retention time file
output_sop	Output pseudo sop file
col_ik	Name of the InChIKey in mgf
col_rt	Name of the retention time in mgf
col_sm	Name of the SMILES in mgf
name_inchikey	Name of the InChIKey in file
name_rt	Name of the retention time in file
name_smiles	Name of the SMILES in file
unit_rt	Unit of the retention time. Must be "seconds" or "minutes"

Value

The path to the prepared retention time library

Examples

## Not run: 
tima:::copy_backbone()
go_to_cache()
prepare_libraries_rt()
unlink("data", recursive = TRUE)

## End(Not run)

taxonomicallyinformedannotation/tima-r documentation built on Dec. 20, 2024, 9:32 a.m.