import_dataset_in_long_format: For advanced users: A generic function for importing data in...

In ftwkoopmans/msdap: Mass Spectrometry Downstream Analysis Pipeline

For advanced users: A generic function for importing data in long-format, typically used for DIA data.

Description

Refer to the implementation of import_dataset_spectronaut for an example on how to use this function. don't forget to set either "dia" or "dda" for dataset$acquisition_mode downstream if you implement this.

Usage

import_dataset_in_long_format(
  filename = NULL,
  x = NULL,
  attributes_required = list(),
  attributes_optional = list(),
  confidence_threshold = 0.01,
  remove_peptides_never_above_confidence_threshold = TRUE,
  select_unique_precursor_per_modseq = TRUE,
  custom_func_manipulate_DT_onload = NULL,
  return_decoys = TRUE,
  do_plot = TRUE
)

Arguments

filename	the full file path of the input file. Either supply a filename, or a data table
x	input data table as a data.frame (or tibble, or data.table). Either supply a filename, or a data table
attributes_required	a list of attributes that must be present in the input file (eg; sample names, peptide IDs, intensity values, etc.)
attributes_optional	a list of optional attributes that we can do without downstream, like m/z
confidence_threshold	confidence score threshold at which a peptide is considered 'identified' (target value must be lesser than or equals)
remove_peptides_never_above_confidence_threshold	set to true to remove all target peptides that never pass the confidence score threshold
select_unique_precursor_per_modseq	if multiple precursors are available for a modified sequence (eg; charge 2 and 3), should we make an effort to select the best or just return all of them ?
custom_func_manipulate_DT_onload	!expert use only! (there is intricate interplay between such pre-filtering and the code in this function); provide a function that manipulates the data.table after load. example implementation in the fragpipe parser.
return_decoys	logical indicating whether to return decoy peptides. Should be set to FALSE, and if enabled, make sure to manually remove the decoys from the peptides tibble before running the quickstart function!
do_plot	logical indicating whether to create QC plots that are shown in the downstream PDF report (if enabled)

ftwkoopmans/msdap documentation built on March 5, 2025, 12:15 a.m.