fragpipe_peptideresults_to_dataset: From FragPipe peptide result table to an MS-DAP dataset

In ftwkoopmans/msdap: Mass Spectrometry Downstream Analysis Pipeline

From FragPipe peptide result table to an MS-DAP dataset

Description

After composing a protein_id,peptide_id,sample_id,intensity,etc... table upstream, fix protein identifiers, transform RT from seconds to minutes, transform intensity to log2, collapses peptides by plainseq/modseq and finally construct a dataset.

Usage

fragpipe_peptideresults_to_dataset(
  tib_result,
  acquisition_mode,
  confidence_threshold,
  collapse_peptide_by
)

Arguments

tib_result	peptide table composed at the end of import_dataset_fragpipe_ionquant() or import_dataset_fragpipe_quantfiles()
acquisition_mode	see import_dataset_fragpipe_ionquant()
confidence_threshold	see import_dataset_fragpipe_ionquant()
collapse_peptide_by	see import_dataset_fragpipe_ionquant()

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