calculateIsotopeFraction: Calculates the incorporated isotope fraction

In marcpaga/pulsedSilac: Analysis of pulsed-SILAC quantitative proteomics data

Description

Calculates the fraction of an isotope ratio using the following formula:

The ratio should be calculated as:

Usage

calculateIsotopeFraction(x, ...)

## S4 method for signature 'SilacProteinExperiment'
calculateIsotopeFraction(
  x,
  ratioAssay = "ratio",
  oldIsoAssay,
  newIsoAssay,
  earlyTimepoints,
  lateTimepoints,
  conditionCol
)

## S4 method for signature 'SilacPeptideExperiment'
calculateIsotopeFraction(
  x,
  ratioAssay = "ratio",
  oldIsoAssay,
  newIsoAssay,
  earlyTimepoints,
  lateTimepoints,
  conditionCol
)

## S4 method for signature 'SilacProteomicsExperiment'
calculateIsotopeFraction(
  x,
  ratioAssay = "ratio",
  oldIsoAssay,
  newIsoAssay,
  earlyTimepoints,
  lateTimepoints,
  conditionCol
)

Arguments

x	A SilacProteinExperiment, SilacPeptideExperiment or a SilacProteomicsExperiment object.
...	Unused.
ratioAssay	A character with the assay name that has the ratio data.
oldIsoAssay	A character with the assay name that has the new isotope intensity data.
newIsoAssay	A character with the assay name that has the old isotope intensity data.
earlyTimepoints	A numeric indicating which timepoints should be considered early.
lateTimepoints	A numeric indicating which timepoints should be considered late.
conditionCol	A character indicating which column of the colData data.frame indicates the different conditions.

Details

If oldIsoAssay and newIsoAssay arguments are given, then the earlyTimepoints and lateTiempoints arguments can be used. These can be used for example if certain proteins do not have any new isotope intensity during the early timepoint. Because of that, no ratio can be calculated and could lead to additional missing values. If old isotope intensity is detected, then a fraction of 0 for new isotope is given. Same principle applies for the late timepoint but with the isotopes in reverse.

Value

a SilacProteinExperiment, SilacPeptideExperiment or SilacProteomicsExperiment object with additional assays named "fraction".

Examples

data('wormsPE')
calculateIsotopeFraction(wormsPE)

marcpaga/pulsedSilac documentation built on March 11, 2020, 8:49 p.m.