Description Usage Arguments Details Value Examples

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

The ratio should be calculated as:

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 | ```
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
)
``` |

`x` |
A |

`...` |
Unused. |

`ratioAssay` |
A |

`oldIsoAssay` |
A |

`newIsoAssay` |
A |

`earlyTimepoints` |
A |

`lateTimepoints` |
A |

`conditionCol` |
A |

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.

a `SilacProteinExperiment`

, `SilacPeptideExperiment`

or
`SilacProteomicsExperiment`

object with additional assays named
"fraction".

1 2 | ```
data('wormsPE')
calculateIsotopeFraction(wormsPE)
``` |

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