import_dataset_diann: Import a label-free proteomics dataset from DIA-NN

In ftwkoopmans/msdap: Mass Spectrometry Downstream Analysis Pipeline

Import a label-free proteomics dataset from DIA-NN

Description

Import a label-free proteomics dataset from DIA-NN

Usage

import_dataset_diann(
  filename,
  confidence_threshold = 0.01,
  use_normalized_intensities = FALSE,
  use_irt = TRUE,
  do_plot = TRUE
)

Arguments

filename	the full file path of the DIA-NN report; this can be either the report.tsv file or the report.parquet file (new since DIA-NN 1.9.1)
confidence_threshold	confidence score threshold at which a peptide is considered 'identified', default: 0.01 (target value must be lesser than or equals)
use_normalized_intensities	use the abundance values as-is (recommended) or those normalized by DIA-NN
use_irt	logical indicating whether to use standardized (IRT) or the empirical (RT) retention times
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.