calculateIsotopeFraction {pulsedSilac} | R Documentation

## Calculates the incorporated isotope fraction

### 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)

[Package pulsedSilac version 1.6.0 Index]