import_ProteinPilot: Import SCIEX ProteinPilot data

Description Usage Arguments Value

Description

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

Usage

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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,
  as.data.table = F
)

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 Nov. 25, 2021, 1:18 p.m.