Prepare libraries of retention times — prepare_libraries

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

if (FALSE) { # \dontrun{
tima:::copy_backbone()
go_to_cache()
prepare_libraries_rt()
unlink("data", recursive = TRUE)
} # }