FSWE.scaleIntensities: FSWE.scaleIntensities

In IFIproteomics/LFQbench: Label Free Quantitation benchmark package

FSWE.scaleIntensities

Description

It scales FSWE-processed files to a common intensity scale defined by one software reference.

Usage

FSWE.scaleIntensities(working_dir = LFQbench.Config$DataRootFolder,
  fileModelingPattern = "_peptides", filesToModelPattern = ".[\\.].",
  filesNotToModelPattern = "FILE_I_DONT_WANT_TO_HAVE",
  softwareReference = "PeakView", softToModelMap = list(),
  softwareLabels = NULL, outputFileNameSuffix = NULL)

Arguments

working_dir	LFQbench-root directory with the subfolder input containing files processed by FSWE that you want to scale
fileModelingPattern	pattern for files you want to use for modeling
filesToModelPattern	pattern for files to apply the scaling models
softwareReference	software name for scaling reference

Details

Assumption: since we lose at this point the peak retention times, we will assume in this script that most of the peaks detected by different software tools match.

IFIproteomics/LFQbench documentation built on March 2, 2023, 9:45 a.m.