Description Usage Arguments Details Value Examples
Method to apply turnover models on protein/peptide data
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 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51  modelTurnover(x, ...)
## S4 method for signature 'SilacProteinExperiment'
modelTurnover(
x,
assayName = "fraction",
formula = "fraction ~ 1exp(k*t)",
start = list(k = 0.02),
robust = FALSE,
mode = "protein",
verbose = FALSE,
returnModel = FALSE,
conditionCol,
timeCol,
silent = TRUE,
...
)
## S4 method for signature 'SilacPeptideExperiment'
modelTurnover(
x,
assayName = "fraction",
formula = "fraction ~ 1exp(k*t)",
start = list(k = 0.02),
robust = FALSE,
mode = c("grouped", "peptide"),
verbose = FALSE,
returnModel = FALSE,
conditionCol,
timeCol,
proteinCol,
silent = TRUE,
...
)
## S4 method for signature 'SilacProteomicsExperiment'
modelTurnover(
x,
assayName = "fraction",
formula = "fraction ~ 1exp(k*t)",
start = list(k = 0.02),
robust = FALSE,
mode = c("protein", "grouped", "peptide"),
verbose = FALSE,
returnModel = FALSE,
conditionCol,
timeCol,
proteinCol,
silent = TRUE,
...
)

x 
A 
... 
further parameters passed into 
assayName 

formula 

start 
named 
robust 

mode 

verbose 

returnModel 

conditionCol 

timeCol 

silent 

proteinCol 

The nls and nlrob functions have many arguments that can be tunned for parameter fitting. Unfortunately, not all the possible argument combinations have been tested. It is recommended to first test one model with the desired parameters with silent = FALSE to see that it runs smoothly and then run the whole proteome with silent = TRUE to supress failed convergence errors. For example, some methods for nlrob use upper and lower bounds instead of start.
Please open an issue on github if the function is having trouble with a particular argument.
For robust modelling the method 'CM' and 'mtl' are not yet supported.
A named list
with either model metrics in matrices or the
model objects.
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