R: Estimate protein/peptide turnover

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]