get_procfuncs – prolfquapp

Get all processing functions from all packages

Description

Get all processing functions from all packages

Usage

get_procfuncs(
  function_name = "prolfqua_preprocess_functions",
  prefix = "prolfqua"
)

Arguments

function_name The name of the function to get

prefix The prefix of the package names

Value

A list of processing functions

Examples

library("prolfquapp")

get_procfuncs()

$prolfquapp.DIANN
$prolfquapp.DIANN$get_files
[1] "prolfquapp::get_DIANN_files"

$prolfquapp.DIANN$preprocess
[1] "prolfquapp::preprocess_DIANN"

$prolfquapp.DIANN$extra_args
[1] "list(q_value = 0.01, hierarchy_depth = 1)"

$prolfquapp.DIANN$dataset
[1] "prolfquapp::dataset_template_diann"


$prolfquapp.DIANN_PEPTIDE
$prolfquapp.DIANN_PEPTIDE$get_files
[1] "prolfquapp::get_DIANN_files"

$prolfquapp.DIANN_PEPTIDE$preprocess
[1] "prolfquapp::preprocess_DIANN"

$prolfquapp.DIANN_PEPTIDE$extra_args
[1] "list(q_value = 0.01, hierarchy_depth = 2)"

$prolfquapp.DIANN_PEPTIDE$dataset
[1] "prolfquapp::dataset_template_diann"


$prolfquapp.FP_TMT
$prolfquapp.FP_TMT$get_files
[1] "prolfquapp::get_FP_PSM_files"

$prolfquapp.FP_TMT$preprocess
[1] "prolfquapp::preprocess_FP_PSM"

$prolfquapp.FP_TMT$extra_args
[1] "list(purity_threshold = 0.5, PeptideProphetProb = 0.9, hierarchy_depth = 1)"

$prolfquapp.FP_TMT$dataset
[1] "prolfquapp::dataset_template_FP_TMT"


$prolfquapp.FP_TMT_PEPTIDE
$prolfquapp.FP_TMT_PEPTIDE$get_files
[1] "prolfquapp::get_FP_PSM_files"

$prolfquapp.FP_TMT_PEPTIDE$preprocess
[1] "prolfquapp::preprocess_FP_PSM"

$prolfquapp.FP_TMT_PEPTIDE$extra_args
[1] "list(purity_threshold = 0.5, PeptideProphetProb = 0.9, hierarchy_depth = 2)"

$prolfquapp.FP_TMT_PEPTIDE$dataset
[1] "prolfquapp::dataset_template_FP_TMT"


$prolfquapp.MAXQUANT
$prolfquapp.MAXQUANT$get_files
[1] "prolfquapp::get_MQ_peptide_files"

$prolfquapp.MAXQUANT$preprocess
[1] "prolfquapp::preprocess_MQ_peptide"

$prolfquapp.MAXQUANT$extra_args
[1] "list(hierarchy_depth = 1)"

$prolfquapp.MAXQUANT$dataset
[1] "prolfquapp::dataset_template_MAXQUANT"


$prolfquapp.MAXQUANT_PEPTIDE
$prolfquapp.MAXQUANT_PEPTIDE$get_files
[1] "prolfquapp::get_MQ_peptide_files"

$prolfquapp.MAXQUANT_PEPTIDE$preprocess
[1] "prolfquapp::preprocess_MQ_peptide"

$prolfquapp.MAXQUANT_PEPTIDE$extra_args
[1] "list(hierarchy_depth = 2)"

$prolfquapp.MAXQUANT_PEPTIDE$dataset
[1] "prolfquapp::dataset_template_MAXQUANT"


$prolfquapp.MSSTATS
$prolfquapp.MSSTATS$get_files
[1] "prolfquapp::get_MSstats_files"

$prolfquapp.MSSTATS$preprocess
[1] "prolfquapp::preprocess_MSstats"

$prolfquapp.MSSTATS$extra_args
[1] "list(hierarchy_depth = 1)"

$prolfquapp.MSSTATS$dataset
[1] "prolfquapp::dataset_template_MSSTATS"


$prolfquapp.MSSTATS_PEPTIDE
$prolfquapp.MSSTATS_PEPTIDE$get_files
[1] "prolfquapp::get_MSstats_files"

$prolfquapp.MSSTATS_PEPTIDE$preprocess
[1] "prolfquapp::preprocess_MSstats"

$prolfquapp.MSSTATS_PEPTIDE$extra_args
[1] "list(hierarchy_depth = 2)"

$prolfquapp.MSSTATS_PEPTIDE$dataset
[1] "prolfquapp::dataset_template_MSSTATS"


$prolfquapp.MSSTATS_FP_DIA
$prolfquapp.MSSTATS_FP_DIA$get_files
[1] "prolfquapp::get_MSstats_files"

$prolfquapp.MSSTATS_FP_DIA$preprocess
[1] "prolfquapp::preprocess_MSstats_FPDIA"

$prolfquapp.MSSTATS_FP_DIA$extra_args
[1] "list(hierarchy_depth = 1)"

$prolfquapp.MSSTATS_FP_DIA$dataset
[1] "prolfquapp::dataset_template_MSSTATS"


$prolfquapp.MSSTATS_FP_DIA_PEPTIDE
$prolfquapp.MSSTATS_FP_DIA_PEPTIDE$get_files
[1] "prolfquapp::get_MSstats_files"

$prolfquapp.MSSTATS_FP_DIA_PEPTIDE$preprocess
[1] "prolfquapp::preprocess_MSstats_FPDIA"

$prolfquapp.MSSTATS_FP_DIA_PEPTIDE$extra_args
[1] "list(hierarchy_depth = 2)"

$prolfquapp.MSSTATS_FP_DIA_PEPTIDE$dataset
[1] "prolfquapp::dataset_template_MSSTATS"


$prolfquapp.BGS
$prolfquapp.BGS$get_files
[1] "prolfquapp::get_BGS_files"

$prolfquapp.BGS$preprocess
[1] "prolfquapp::preprocess_BGS"

$prolfquapp.BGS$extra_args
[1] "list(hierarchy_depth = 1)"

$prolfquapp.BGS$dataset
[1] "prolfquapp::dataset_template_BGS"


$prolfquapp.BGS_PEPTIDE
$prolfquapp.BGS_PEPTIDE$get_files
[1] "prolfquapp::get_BGS_files"

$prolfquapp.BGS_PEPTIDE$preprocess
[1] "prolfquapp::preprocess_BGS"

$prolfquapp.BGS_PEPTIDE$extra_args
[1] "list(hierarchy_depth = 2)"

$prolfquapp.BGS_PEPTIDE$dataset
[1] "prolfquapp::dataset_template_BGS"


$prolfquapp.DUMMY
$prolfquapp.DUMMY$get_files
[1] "prolfquapp::get_dummy_files"

$prolfquapp.DUMMY$preprocess
[1] "prolfquapp::preprocess_dummy"

$prolfquapp.DUMMY$extra_args
[1] "list()"


$prolfquapp.MZMINE
$prolfquapp.MZMINE$get_files
[1] "prolfquapp::get_mzMine_files"

$prolfquapp.MZMINE$preprocess
[1] "prolfquapp::preprocess_mzMine"

$prolfquapp.MZMINE$extra_args
[1] "list(annotated = FALSE)"


$prolfquapp.MZMINEannot
$prolfquapp.MZMINEannot$get_files
[1] "prolfquapp::get_mzMine_files"

$prolfquapp.MZMINEannot$preprocess
[1] "prolfquapp::preprocess_mzMine"

$prolfquapp.MZMINEannot$extra_args
[1] "list(annotated = TRUE)"


$prolfquapp.SIM
$prolfquapp.SIM$get_files
[1] "prolfquapp::get_SIM_files"

$prolfquapp.SIM$preprocess
[1] "prolfquapp::preprocess_SIM"

$prolfquapp.SIM$extra_args
[1] "list(hierarchy_depth = 1)"

get_procfuncs("prolfqua_preprocess_functions", "prolfqua")

$prolfquapp.DIANN
$prolfquapp.DIANN$get_files
[1] "prolfquapp::get_DIANN_files"

$prolfquapp.DIANN$preprocess
[1] "prolfquapp::preprocess_DIANN"

$prolfquapp.DIANN$extra_args
[1] "list(q_value = 0.01, hierarchy_depth = 1)"

$prolfquapp.DIANN$dataset
[1] "prolfquapp::dataset_template_diann"


$prolfquapp.DIANN_PEPTIDE
$prolfquapp.DIANN_PEPTIDE$get_files
[1] "prolfquapp::get_DIANN_files"

$prolfquapp.DIANN_PEPTIDE$preprocess
[1] "prolfquapp::preprocess_DIANN"

$prolfquapp.DIANN_PEPTIDE$extra_args
[1] "list(q_value = 0.01, hierarchy_depth = 2)"

$prolfquapp.DIANN_PEPTIDE$dataset
[1] "prolfquapp::dataset_template_diann"


$prolfquapp.FP_TMT
$prolfquapp.FP_TMT$get_files
[1] "prolfquapp::get_FP_PSM_files"

$prolfquapp.FP_TMT$preprocess
[1] "prolfquapp::preprocess_FP_PSM"

$prolfquapp.FP_TMT$extra_args
[1] "list(purity_threshold = 0.5, PeptideProphetProb = 0.9, hierarchy_depth = 1)"

$prolfquapp.FP_TMT$dataset
[1] "prolfquapp::dataset_template_FP_TMT"


$prolfquapp.FP_TMT_PEPTIDE
$prolfquapp.FP_TMT_PEPTIDE$get_files
[1] "prolfquapp::get_FP_PSM_files"

$prolfquapp.FP_TMT_PEPTIDE$preprocess
[1] "prolfquapp::preprocess_FP_PSM"

$prolfquapp.FP_TMT_PEPTIDE$extra_args
[1] "list(purity_threshold = 0.5, PeptideProphetProb = 0.9, hierarchy_depth = 2)"

$prolfquapp.FP_TMT_PEPTIDE$dataset
[1] "prolfquapp::dataset_template_FP_TMT"


$prolfquapp.MAXQUANT
$prolfquapp.MAXQUANT$get_files
[1] "prolfquapp::get_MQ_peptide_files"

$prolfquapp.MAXQUANT$preprocess
[1] "prolfquapp::preprocess_MQ_peptide"

$prolfquapp.MAXQUANT$extra_args
[1] "list(hierarchy_depth = 1)"

$prolfquapp.MAXQUANT$dataset
[1] "prolfquapp::dataset_template_MAXQUANT"


$prolfquapp.MAXQUANT_PEPTIDE
$prolfquapp.MAXQUANT_PEPTIDE$get_files
[1] "prolfquapp::get_MQ_peptide_files"

$prolfquapp.MAXQUANT_PEPTIDE$preprocess
[1] "prolfquapp::preprocess_MQ_peptide"

$prolfquapp.MAXQUANT_PEPTIDE$extra_args
[1] "list(hierarchy_depth = 2)"

$prolfquapp.MAXQUANT_PEPTIDE$dataset
[1] "prolfquapp::dataset_template_MAXQUANT"


$prolfquapp.MSSTATS
$prolfquapp.MSSTATS$get_files
[1] "prolfquapp::get_MSstats_files"

$prolfquapp.MSSTATS$preprocess
[1] "prolfquapp::preprocess_MSstats"

$prolfquapp.MSSTATS$extra_args
[1] "list(hierarchy_depth = 1)"

$prolfquapp.MSSTATS$dataset
[1] "prolfquapp::dataset_template_MSSTATS"


$prolfquapp.MSSTATS_PEPTIDE
$prolfquapp.MSSTATS_PEPTIDE$get_files
[1] "prolfquapp::get_MSstats_files"

$prolfquapp.MSSTATS_PEPTIDE$preprocess
[1] "prolfquapp::preprocess_MSstats"

$prolfquapp.MSSTATS_PEPTIDE$extra_args
[1] "list(hierarchy_depth = 2)"

$prolfquapp.MSSTATS_PEPTIDE$dataset
[1] "prolfquapp::dataset_template_MSSTATS"


$prolfquapp.MSSTATS_FP_DIA
$prolfquapp.MSSTATS_FP_DIA$get_files
[1] "prolfquapp::get_MSstats_files"

$prolfquapp.MSSTATS_FP_DIA$preprocess
[1] "prolfquapp::preprocess_MSstats_FPDIA"

$prolfquapp.MSSTATS_FP_DIA$extra_args
[1] "list(hierarchy_depth = 1)"

$prolfquapp.MSSTATS_FP_DIA$dataset
[1] "prolfquapp::dataset_template_MSSTATS"


$prolfquapp.MSSTATS_FP_DIA_PEPTIDE
$prolfquapp.MSSTATS_FP_DIA_PEPTIDE$get_files
[1] "prolfquapp::get_MSstats_files"

$prolfquapp.MSSTATS_FP_DIA_PEPTIDE$preprocess
[1] "prolfquapp::preprocess_MSstats_FPDIA"

$prolfquapp.MSSTATS_FP_DIA_PEPTIDE$extra_args
[1] "list(hierarchy_depth = 2)"

$prolfquapp.MSSTATS_FP_DIA_PEPTIDE$dataset
[1] "prolfquapp::dataset_template_MSSTATS"


$prolfquapp.BGS
$prolfquapp.BGS$get_files
[1] "prolfquapp::get_BGS_files"

$prolfquapp.BGS$preprocess
[1] "prolfquapp::preprocess_BGS"

$prolfquapp.BGS$extra_args
[1] "list(hierarchy_depth = 1)"

$prolfquapp.BGS$dataset
[1] "prolfquapp::dataset_template_BGS"


$prolfquapp.BGS_PEPTIDE
$prolfquapp.BGS_PEPTIDE$get_files
[1] "prolfquapp::get_BGS_files"

$prolfquapp.BGS_PEPTIDE$preprocess
[1] "prolfquapp::preprocess_BGS"

$prolfquapp.BGS_PEPTIDE$extra_args
[1] "list(hierarchy_depth = 2)"

$prolfquapp.BGS_PEPTIDE$dataset
[1] "prolfquapp::dataset_template_BGS"


$prolfquapp.DUMMY
$prolfquapp.DUMMY$get_files
[1] "prolfquapp::get_dummy_files"

$prolfquapp.DUMMY$preprocess
[1] "prolfquapp::preprocess_dummy"

$prolfquapp.DUMMY$extra_args
[1] "list()"


$prolfquapp.MZMINE
$prolfquapp.MZMINE$get_files
[1] "prolfquapp::get_mzMine_files"

$prolfquapp.MZMINE$preprocess
[1] "prolfquapp::preprocess_mzMine"

$prolfquapp.MZMINE$extra_args
[1] "list(annotated = FALSE)"


$prolfquapp.MZMINEannot
$prolfquapp.MZMINEannot$get_files
[1] "prolfquapp::get_mzMine_files"

$prolfquapp.MZMINEannot$preprocess
[1] "prolfquapp::preprocess_mzMine"

$prolfquapp.MZMINEannot$extra_args
[1] "list(annotated = TRUE)"


$prolfquapp.SIM
$prolfquapp.SIM$get_files
[1] "prolfquapp::get_SIM_files"

$prolfquapp.SIM$preprocess
[1] "prolfquapp::preprocess_SIM"

$prolfquapp.SIM$extra_args
[1] "list(hierarchy_depth = 1)"

get_procfuncs("prolfqua_preprocess_functions", "prolfquapp")

$prolfquapp.DIANN
$prolfquapp.DIANN$get_files
[1] "prolfquapp::get_DIANN_files"

$prolfquapp.DIANN$preprocess
[1] "prolfquapp::preprocess_DIANN"

$prolfquapp.DIANN$extra_args
[1] "list(q_value = 0.01, hierarchy_depth = 1)"

$prolfquapp.DIANN$dataset
[1] "prolfquapp::dataset_template_diann"


$prolfquapp.DIANN_PEPTIDE
$prolfquapp.DIANN_PEPTIDE$get_files
[1] "prolfquapp::get_DIANN_files"

$prolfquapp.DIANN_PEPTIDE$preprocess
[1] "prolfquapp::preprocess_DIANN"

$prolfquapp.DIANN_PEPTIDE$extra_args
[1] "list(q_value = 0.01, hierarchy_depth = 2)"

$prolfquapp.DIANN_PEPTIDE$dataset
[1] "prolfquapp::dataset_template_diann"


$prolfquapp.FP_TMT
$prolfquapp.FP_TMT$get_files
[1] "prolfquapp::get_FP_PSM_files"

$prolfquapp.FP_TMT$preprocess
[1] "prolfquapp::preprocess_FP_PSM"

$prolfquapp.FP_TMT$extra_args
[1] "list(purity_threshold = 0.5, PeptideProphetProb = 0.9, hierarchy_depth = 1)"

$prolfquapp.FP_TMT$dataset
[1] "prolfquapp::dataset_template_FP_TMT"


$prolfquapp.FP_TMT_PEPTIDE
$prolfquapp.FP_TMT_PEPTIDE$get_files
[1] "prolfquapp::get_FP_PSM_files"

$prolfquapp.FP_TMT_PEPTIDE$preprocess
[1] "prolfquapp::preprocess_FP_PSM"

$prolfquapp.FP_TMT_PEPTIDE$extra_args
[1] "list(purity_threshold = 0.5, PeptideProphetProb = 0.9, hierarchy_depth = 2)"

$prolfquapp.FP_TMT_PEPTIDE$dataset
[1] "prolfquapp::dataset_template_FP_TMT"


$prolfquapp.MAXQUANT
$prolfquapp.MAXQUANT$get_files
[1] "prolfquapp::get_MQ_peptide_files"

$prolfquapp.MAXQUANT$preprocess
[1] "prolfquapp::preprocess_MQ_peptide"

$prolfquapp.MAXQUANT$extra_args
[1] "list(hierarchy_depth = 1)"

$prolfquapp.MAXQUANT$dataset
[1] "prolfquapp::dataset_template_MAXQUANT"


$prolfquapp.MAXQUANT_PEPTIDE
$prolfquapp.MAXQUANT_PEPTIDE$get_files
[1] "prolfquapp::get_MQ_peptide_files"

$prolfquapp.MAXQUANT_PEPTIDE$preprocess
[1] "prolfquapp::preprocess_MQ_peptide"

$prolfquapp.MAXQUANT_PEPTIDE$extra_args
[1] "list(hierarchy_depth = 2)"

$prolfquapp.MAXQUANT_PEPTIDE$dataset
[1] "prolfquapp::dataset_template_MAXQUANT"


$prolfquapp.MSSTATS
$prolfquapp.MSSTATS$get_files
[1] "prolfquapp::get_MSstats_files"

$prolfquapp.MSSTATS$preprocess
[1] "prolfquapp::preprocess_MSstats"

$prolfquapp.MSSTATS$extra_args
[1] "list(hierarchy_depth = 1)"

$prolfquapp.MSSTATS$dataset
[1] "prolfquapp::dataset_template_MSSTATS"


$prolfquapp.MSSTATS_PEPTIDE
$prolfquapp.MSSTATS_PEPTIDE$get_files
[1] "prolfquapp::get_MSstats_files"

$prolfquapp.MSSTATS_PEPTIDE$preprocess
[1] "prolfquapp::preprocess_MSstats"

$prolfquapp.MSSTATS_PEPTIDE$extra_args
[1] "list(hierarchy_depth = 2)"

$prolfquapp.MSSTATS_PEPTIDE$dataset
[1] "prolfquapp::dataset_template_MSSTATS"


$prolfquapp.MSSTATS_FP_DIA
$prolfquapp.MSSTATS_FP_DIA$get_files
[1] "prolfquapp::get_MSstats_files"

$prolfquapp.MSSTATS_FP_DIA$preprocess
[1] "prolfquapp::preprocess_MSstats_FPDIA"

$prolfquapp.MSSTATS_FP_DIA$extra_args
[1] "list(hierarchy_depth = 1)"

$prolfquapp.MSSTATS_FP_DIA$dataset
[1] "prolfquapp::dataset_template_MSSTATS"


$prolfquapp.MSSTATS_FP_DIA_PEPTIDE
$prolfquapp.MSSTATS_FP_DIA_PEPTIDE$get_files
[1] "prolfquapp::get_MSstats_files"

$prolfquapp.MSSTATS_FP_DIA_PEPTIDE$preprocess
[1] "prolfquapp::preprocess_MSstats_FPDIA"

$prolfquapp.MSSTATS_FP_DIA_PEPTIDE$extra_args
[1] "list(hierarchy_depth = 2)"

$prolfquapp.MSSTATS_FP_DIA_PEPTIDE$dataset
[1] "prolfquapp::dataset_template_MSSTATS"


$prolfquapp.BGS
$prolfquapp.BGS$get_files
[1] "prolfquapp::get_BGS_files"

$prolfquapp.BGS$preprocess
[1] "prolfquapp::preprocess_BGS"

$prolfquapp.BGS$extra_args
[1] "list(hierarchy_depth = 1)"

$prolfquapp.BGS$dataset
[1] "prolfquapp::dataset_template_BGS"


$prolfquapp.BGS_PEPTIDE
$prolfquapp.BGS_PEPTIDE$get_files
[1] "prolfquapp::get_BGS_files"

$prolfquapp.BGS_PEPTIDE$preprocess
[1] "prolfquapp::preprocess_BGS"

$prolfquapp.BGS_PEPTIDE$extra_args
[1] "list(hierarchy_depth = 2)"

$prolfquapp.BGS_PEPTIDE$dataset
[1] "prolfquapp::dataset_template_BGS"


$prolfquapp.DUMMY
$prolfquapp.DUMMY$get_files
[1] "prolfquapp::get_dummy_files"

$prolfquapp.DUMMY$preprocess
[1] "prolfquapp::preprocess_dummy"

$prolfquapp.DUMMY$extra_args
[1] "list()"


$prolfquapp.MZMINE
$prolfquapp.MZMINE$get_files
[1] "prolfquapp::get_mzMine_files"

$prolfquapp.MZMINE$preprocess
[1] "prolfquapp::preprocess_mzMine"

$prolfquapp.MZMINE$extra_args
[1] "list(annotated = FALSE)"


$prolfquapp.MZMINEannot
$prolfquapp.MZMINEannot$get_files
[1] "prolfquapp::get_mzMine_files"

$prolfquapp.MZMINEannot$preprocess
[1] "prolfquapp::preprocess_mzMine"

$prolfquapp.MZMINEannot$extra_args
[1] "list(annotated = TRUE)"


$prolfquapp.SIM
$prolfquapp.SIM$get_files
[1] "prolfquapp::get_SIM_files"

$prolfquapp.SIM$preprocess
[1] "prolfquapp::preprocess_SIM"

$prolfquapp.SIM$extra_args
[1] "list(hierarchy_depth = 1)"

get_procfuncs("prolfqua_preprocess_functions", "prolfquapp")

$prolfquapp.DIANN
$prolfquapp.DIANN$get_files
[1] "prolfquapp::get_DIANN_files"

$prolfquapp.DIANN$preprocess
[1] "prolfquapp::preprocess_DIANN"

$prolfquapp.DIANN$extra_args
[1] "list(q_value = 0.01, hierarchy_depth = 1)"

$prolfquapp.DIANN$dataset
[1] "prolfquapp::dataset_template_diann"


$prolfquapp.DIANN_PEPTIDE
$prolfquapp.DIANN_PEPTIDE$get_files
[1] "prolfquapp::get_DIANN_files"

$prolfquapp.DIANN_PEPTIDE$preprocess
[1] "prolfquapp::preprocess_DIANN"

$prolfquapp.DIANN_PEPTIDE$extra_args
[1] "list(q_value = 0.01, hierarchy_depth = 2)"

$prolfquapp.DIANN_PEPTIDE$dataset
[1] "prolfquapp::dataset_template_diann"


$prolfquapp.FP_TMT
$prolfquapp.FP_TMT$get_files
[1] "prolfquapp::get_FP_PSM_files"

$prolfquapp.FP_TMT$preprocess
[1] "prolfquapp::preprocess_FP_PSM"

$prolfquapp.FP_TMT$extra_args
[1] "list(purity_threshold = 0.5, PeptideProphetProb = 0.9, hierarchy_depth = 1)"

$prolfquapp.FP_TMT$dataset
[1] "prolfquapp::dataset_template_FP_TMT"


$prolfquapp.FP_TMT_PEPTIDE
$prolfquapp.FP_TMT_PEPTIDE$get_files
[1] "prolfquapp::get_FP_PSM_files"

$prolfquapp.FP_TMT_PEPTIDE$preprocess
[1] "prolfquapp::preprocess_FP_PSM"

$prolfquapp.FP_TMT_PEPTIDE$extra_args
[1] "list(purity_threshold = 0.5, PeptideProphetProb = 0.9, hierarchy_depth = 2)"

$prolfquapp.FP_TMT_PEPTIDE$dataset
[1] "prolfquapp::dataset_template_FP_TMT"


$prolfquapp.MAXQUANT
$prolfquapp.MAXQUANT$get_files
[1] "prolfquapp::get_MQ_peptide_files"

$prolfquapp.MAXQUANT$preprocess
[1] "prolfquapp::preprocess_MQ_peptide"

$prolfquapp.MAXQUANT$extra_args
[1] "list(hierarchy_depth = 1)"

$prolfquapp.MAXQUANT$dataset
[1] "prolfquapp::dataset_template_MAXQUANT"


$prolfquapp.MAXQUANT_PEPTIDE
$prolfquapp.MAXQUANT_PEPTIDE$get_files
[1] "prolfquapp::get_MQ_peptide_files"

$prolfquapp.MAXQUANT_PEPTIDE$preprocess
[1] "prolfquapp::preprocess_MQ_peptide"

$prolfquapp.MAXQUANT_PEPTIDE$extra_args
[1] "list(hierarchy_depth = 2)"

$prolfquapp.MAXQUANT_PEPTIDE$dataset
[1] "prolfquapp::dataset_template_MAXQUANT"


$prolfquapp.MSSTATS
$prolfquapp.MSSTATS$get_files
[1] "prolfquapp::get_MSstats_files"

$prolfquapp.MSSTATS$preprocess
[1] "prolfquapp::preprocess_MSstats"

$prolfquapp.MSSTATS$extra_args
[1] "list(hierarchy_depth = 1)"

$prolfquapp.MSSTATS$dataset
[1] "prolfquapp::dataset_template_MSSTATS"


$prolfquapp.MSSTATS_PEPTIDE
$prolfquapp.MSSTATS_PEPTIDE$get_files
[1] "prolfquapp::get_MSstats_files"

$prolfquapp.MSSTATS_PEPTIDE$preprocess
[1] "prolfquapp::preprocess_MSstats"

$prolfquapp.MSSTATS_PEPTIDE$extra_args
[1] "list(hierarchy_depth = 2)"

$prolfquapp.MSSTATS_PEPTIDE$dataset
[1] "prolfquapp::dataset_template_MSSTATS"


$prolfquapp.MSSTATS_FP_DIA
$prolfquapp.MSSTATS_FP_DIA$get_files
[1] "prolfquapp::get_MSstats_files"

$prolfquapp.MSSTATS_FP_DIA$preprocess
[1] "prolfquapp::preprocess_MSstats_FPDIA"

$prolfquapp.MSSTATS_FP_DIA$extra_args
[1] "list(hierarchy_depth = 1)"

$prolfquapp.MSSTATS_FP_DIA$dataset
[1] "prolfquapp::dataset_template_MSSTATS"


$prolfquapp.MSSTATS_FP_DIA_PEPTIDE
$prolfquapp.MSSTATS_FP_DIA_PEPTIDE$get_files
[1] "prolfquapp::get_MSstats_files"

$prolfquapp.MSSTATS_FP_DIA_PEPTIDE$preprocess
[1] "prolfquapp::preprocess_MSstats_FPDIA"

$prolfquapp.MSSTATS_FP_DIA_PEPTIDE$extra_args
[1] "list(hierarchy_depth = 2)"

$prolfquapp.MSSTATS_FP_DIA_PEPTIDE$dataset
[1] "prolfquapp::dataset_template_MSSTATS"


$prolfquapp.BGS
$prolfquapp.BGS$get_files
[1] "prolfquapp::get_BGS_files"

$prolfquapp.BGS$preprocess
[1] "prolfquapp::preprocess_BGS"

$prolfquapp.BGS$extra_args
[1] "list(hierarchy_depth = 1)"

$prolfquapp.BGS$dataset
[1] "prolfquapp::dataset_template_BGS"


$prolfquapp.BGS_PEPTIDE
$prolfquapp.BGS_PEPTIDE$get_files
[1] "prolfquapp::get_BGS_files"

$prolfquapp.BGS_PEPTIDE$preprocess
[1] "prolfquapp::preprocess_BGS"

$prolfquapp.BGS_PEPTIDE$extra_args
[1] "list(hierarchy_depth = 2)"

$prolfquapp.BGS_PEPTIDE$dataset
[1] "prolfquapp::dataset_template_BGS"


$prolfquapp.DUMMY
$prolfquapp.DUMMY$get_files
[1] "prolfquapp::get_dummy_files"

$prolfquapp.DUMMY$preprocess
[1] "prolfquapp::preprocess_dummy"

$prolfquapp.DUMMY$extra_args
[1] "list()"


$prolfquapp.MZMINE
$prolfquapp.MZMINE$get_files
[1] "prolfquapp::get_mzMine_files"

$prolfquapp.MZMINE$preprocess
[1] "prolfquapp::preprocess_mzMine"

$prolfquapp.MZMINE$extra_args
[1] "list(annotated = FALSE)"


$prolfquapp.MZMINEannot
$prolfquapp.MZMINEannot$get_files
[1] "prolfquapp::get_mzMine_files"

$prolfquapp.MZMINEannot$preprocess
[1] "prolfquapp::preprocess_mzMine"

$prolfquapp.MZMINEannot$extra_args
[1] "list(annotated = TRUE)"


$prolfquapp.SIM
$prolfquapp.SIM$get_files
[1] "prolfquapp::get_SIM_files"

$prolfquapp.SIM$preprocess
[1] "prolfquapp::preprocess_SIM"

$prolfquapp.SIM$extra_args
[1] "list(hierarchy_depth = 1)"

get_procfuncs("prolfqua_preprocess_functions", "xdx")

NULL