calc.delta.score

calc.pep.delta.score

filterSpectraDeltaScore

my.data

min.delta.score

If TRUE, spectra below the min.prob threshold are not just set as 'use.for.quant=FALSE' but removed.

do.remove


  Calculates delta score from raw search engine score by substracting the best matching hit with the second best matching.
  data needs to have not only the best hit per spectrum, but multiple, to be able to calculate the delta score.
  filterSpectraDeltaScore calls <code>calc.delta.score</code> and filters spectra below a minum delta score.

isobar provides methods for preprocessing, normalization, and
report generation for the analysis of quantitative mass spectrometry
proteomics data labeled with isobaric tags, such as iTRAQ and TMT.
Features modules for integrating and validating PTM-centric datasets
(isobar-PTM). More information on http://www.ms-isobar.org.

Florian P Breitwieser

isobar

Analysis and quantitation of isobarically tagged MSMS proteomics data

calc.delta.score function

Calculates delta score from raw search engine score by substracting the best matching hit with the second best matching.
  data needs to have not only the best hit per spectrum, but multiple, to be able to calculate the delta score.
  filterSpectraDeltaScore calls <code>calc.delta.score</code> and filters spectra below a minum delta score.

calc.delta.score: Calculate Delta Score from Ion Score

Description

Usage

Arguments

Value