modelTurnover {pulsedSilac} | R Documentation

## Estimate protein/peptide turnover

### Description

Method to apply turnover models on protein/peptide data

### Usage

    modelTurnover(x, ...)

    ## S4 method for signature 'SilacProteinExperiment'
    modelTurnover(
      x,
      assayName = "fraction",
      formula = "fraction ~ 1-exp(-k*t)",
      start = list(k = 0.02),
      robust = FALSE,
      mode = "protein",
      verbose = FALSE,
      returnModel = FALSE,
      conditionCol,
      timeCol,
      ...
    )

    ## S4 method for signature 'SilacPeptideExperiment'
    modelTurnover(
      x,
      assayName = "fraction",
      formula = "fraction ~ 1-exp(-k*t)",
      start = list(k = 0.02),
      robust = FALSE,
      mode = c("grouped", "peptide"),
      verbose = FALSE,
      returnModel = FALSE,
      conditionCol,
      timeCol,
      proteinCol,
      ...
    )

    ## S4 method for signature 'SilacProteomicsExperiment'
    modelTurnover(
      x,
      assayName = "fraction",
      formula = "fraction ~ 1-exp(-k*t)",
      start = list(k = 0.02),
      robust = FALSE,
      mode = c("protein", "grouped", "peptide"),
      verbose = FALSE,
      returnModel = FALSE,
      conditionCol,
      timeCol,
      proteinCol,
      ...
    )

### Arguments

`x` | A `SilacProteinExperiment`, `SilacPeptideExperiment` or `SilacProteomicsExperiment` object.
`...` | further parameters passed into `nls` or `nlrob`.
`assayName` | `character` indicating which assay to use as data input for the model.
`formula` | `formula` to be used. Time must always be named "t" and the data must be named "fraction".
`start` | named `list` with the initical values for the parameters in formula.
`robust` | `logical` indicating if robust modelling from the `robustbase` package should be used.
`mode` | `character` indicating which type of data should be used. Can be "protein": one model per protein; "grouped": one model per protein using peptide data; "peptide" one model per peptide.
`verbose` | `logical` indicating if a progress bar should be printed.
`returnModel` | `logical` indicating if the model objects should be returned also in the output.
`conditionCol` | `character` indicating which column of colData(x) describes the conditions.
`timeCol` | `character` indicating which column of colData(x) describes time.
`proteinCol` | `character` indicating which column of rowData(x) describes the assigned protein to a peptide. (Only for peptide data)

### Value

A named `list` with either model metrics in matrices or the model objects.

### Examples

    data('wormsPE')
    wormsPE <- calculateIsotopeFraction(wormsPE, ratioAssay = 'ratio')

    modelList <- modelTurnover(x = wormsPE[1:10],
                               assayName = 'fraction',
                               formula = 'fraction ~ 1 - exp(-k*t)',
                               start = list(k = 0.02),
                               mode = 'protein',
                               robust = FALSE,
                               returnModel = TRUE)

[Package pulsedSilac version 1.0.1 Index]