import_OpenSWATH: Import OpenSWATH data

In biospi/deamass: Statistical modelling for mass spectrometry omics

Description

Reads in the output of an OpenSWATH -> PyProphet -> TRIC pipeline.

Usage

import_OpenSWATH(
  file = NULL,
  max.m_score = 0.05,
  use.shared.peptides = FALSE,
  use.decoys = FALSE,
  data = NULL,
  as.data.table = F
)

Arguments

max.m_score	Include only measurements with PyProphet m_score >= than this?
data	Advanced: Rather than specifying a file, you can enter a data.frame preloaded with fread default parameters.
files	A csv file to import.

Value

A data.frame for input into seaMass_sigma.

biospi/deamass documentation built on Nov. 25, 2021, 1:18 p.m.