import_dataset_fragpipe_psm_file: Alternative FragPipe workflow, operates directly on a single...
In ftwkoopmans/msdap: Mass Spectrometry Downstream Analysis Pipeline

import_dataset_fragpipe_psm_file

R Documentation

Alternative FragPipe workflow, operates directly on a single psm.tsv file

Description

For typical FragPipe workflows, import_dataset_fragpipe_ionquant() should be used instead of this function !

This function directly parses data from a psm.tsv file and doesn't use MBR data produced by FragPipe; use this function for legacy FragPipe data OR FragPipe runs where no experiment info was provided at all in the FragPipe workflow tab.

if intensity_sum is set to FALSE, the most abundant PSM per peptide*sample is selected to represent abundance.

Usage

import_dataset_fragpipe_psm_file(
  filename,
  intensity_sum = TRUE,
  acquisition_mode,
  confidence_threshold = 0.01,
  collapse_peptide_by = "sequence_modified"
)

Arguments

`filename`	the full file path of the input file
`intensity_sum`	boolean value whether to take the sum intensity of all PSM per precursor (TRUE, default) or use the value from the PSM with highest abundance (FALSE)
`acquisition_mode`	the type of experiment, should be a string. options: "dda" or "dia"
`confidence_threshold`	confidence score threshold at which a peptide is considered 'identified' (target value must be lesser than or equals)
`collapse_peptide_by`	if multiple data points are available for a peptide in a sample, at what level should these be combined? options: "sequence_modified" (recommended default), "sequence_plain", ""