import_ProteinPilot: Import SCIEX ProteinPilot data

In biospi/deamass: Statistical modelling for mass spectrometry omics

Import SCIEX ProteinPilot data

Description

Reads in a SCIEX ProteinPilot PeptideSummary.txt file for processing with seaMass_sigma.

Usage

import_ProteinPilot(
  file = NULL,
  min.conf = "auto",
  use.decoys = FALSE,
  use.shared.peptides = FALSE,
  use.discordant.peptide.type = FALSE,
  use.no.itraq = FALSE,
  use.weak.signal = FALSE,
  data = NULL
)

Arguments

file	Location of the PeptideSummary.txt file.
min.conf	Measurements with peptide ID confidence less than min.conf (between 0 - 100) are filtered out. The default "auto" uses the ProteinPilot default threshold.
data	Advanced: Rather than specifying file, you can enter a data.frame preloaded with fread default parameters.
shared	Include shared peptides?
filter	Other filters to use, which can include "discordant peptide type", "no iTRAQ" and "weak signal"

Value

A data.frame for input into seaMass_sigma.

biospi/deamass documentation built on May 20, 2023, 3:30 a.m.