import_expressionset: Import a label-free proteomics dataset from a peptide-level...

In ftwkoopmans/msdap: Mass Spectrometry Downstream Analysis Pipeline

Import a label-free proteomics dataset from a peptide-level Biobase ExpressionSet object

Description

provided mostly for compatability with results from prior bioinformatic analyses, as it is preferred to import raw data files.

Usage

import_expressionset(
  eset,
  column_fdata_protein_id = "prot.id",
  column_pdata_sample_group = "condition",
  acquisition_mode = "dda",
  is_log2 = FALSE
)

Arguments

eset	a Biobase ExpressionSet containing peptide data
column_fdata_protein_id	the column name in Biobase::fData() that holds the protein_id
column_pdata_sample_group	the column name in Biobase::pData() that holds the sample group/condition
acquisition_mode	the type of label-free data. options: 'dda' or 'dia'
is_log2	logical indicating whether the provided intensities are already log2 transformed

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