void TransformationModelLowess::getDefaultParameters(Param& params)
{
params.clear();
params.setValue("span", 2/3.0, "Fraction of datapoints (f) to use for each local regression (determines the amount of smoothing). Choosing this parameter in the range .2 to .8 usually results in a good fit.");
params.setMinFloat("span", 0.0);
params.setMaxFloat("span", 1.0);
params.setValue("num_iterations", 3, "Number of rubstifying iterations for lowess fitting.");
params.setMinInt("num_iterations", 0);
params.setValue("delta", -1.0, "Nonnegative parameter which may be used to save computations (recommended value is 0.01 of the range of the input, e.g. for data ranging from 1000 seconds to 2000 seconds, it could be set to 10). Setting a negative value will automatically do this.");
params.setValue("interpolation_type", "cspline", "Method to use for interpolation between datapoints computed by lowess. 'linear': Linear interpolation. 'cspline': Use the cubic spline for interpolation. 'akima': Use an akima spline for interpolation");
params.setValidStrings("interpolation_type", ListUtils::create<String>("linear,cspline,akima"));
params.setValue("extrapolation_type", "four-point-linear", "Method to use for extrapolation outside the data range. 'two-point-linear': Uses a line through the first and last point to extrapolate. 'four-point-linear': Uses a line through the first and second point to extrapolate in front and and a line through the last and second-to-last point in the end. 'global-linear': Uses a linear regression to fit a line through all data points and use it for interpolation.");
StringList etypes = ListUtils::create<String>("two-point-linear,four-point-linear,global-linear");
params.setValidStrings("extrapolation_type", etypes);
}
// create prameters for sections (set default values and restrictions)
Param getSubsectionDefaults_(const String & section) const
{
Param defaults;
//--------------------------------------------------
// section labels
//--------------------------------------------------
if (section == "labels")
{
// create labels that can be chosen in section "sample/labels"
defaults.setValue("Arg6", 6.0201290268, "Arg6 mass shift", StringList::create("advanced"));
defaults.setMinFloat("Arg6", 0.0);
defaults.setValue("Arg10", 10.008268600, "Arg10 mass shift", StringList::create("advanced"));
defaults.setMinFloat("Arg10", 0.0);
defaults.setValue("Lys4", 4.0251069836, "Lys4 mass shift", StringList::create("advanced"));
defaults.setMinFloat("Lys4", 0.0);
defaults.setValue("Lys6", 6.0201290268, "Lys6 mass shift", StringList::create("advanced"));
defaults.setMinFloat("Lys6", 0.0);
defaults.setValue("Lys8", 8.0141988132, "Lys8 mass shift", StringList::create("advanced"));
defaults.setMinFloat("Lys8", 0.0);
defaults.setValue("dICPL4", 4.025107, "mass difference between isotope-coded protein labels ICPL 4 and ICPL 0", StringList::create("advanced"));
defaults.setMinFloat("dICPL4", 0.0);
defaults.setValue("dICPL6", 6.020129, "mass difference between isotope-coded protein labels ICPL 6 and ICPL 0", StringList::create("advanced"));
defaults.setMinFloat("dICPL6", 0.0);
defaults.setValue("dICPL10", 10.045236, "mass difference between isotope-coded protein labels ICPL 10 and ICPL 0", StringList::create("advanced"));
defaults.setMinFloat("dICPL10", 0.0);
defaults.setValue("Methyl4", 4.0202, "Methyl4 mass shift", StringList::create("advanced"));
defaults.setMinFloat("Methyl4", 0.0);
defaults.setValue("Methyl8", 8.0202, "Methyl8 mass shift", StringList::create("advanced"));
defaults.setMinFloat("Methyl8", 0.0);
defaults.setValue("Methyl12", 12.0202, "Methyl12 mass shift", StringList::create("advanced"));
defaults.setMinFloat("Methyl12", 0.0);
defaults.setValue("Methyl16", 16.0202, "Methyl16 mass shift", StringList::create("advanced"));
defaults.setMinFloat("Methyl16", 0.0);
defaults.setValue("Methyl24", 24.0202, "Methyl24 mass shift", StringList::create("advanced"));
defaults.setMinFloat("Methyl24", 0.0);
defaults.setValue("Methyl32", 32.0202, "Methyl32 mass shift", StringList::create("advanced"));
defaults.setMinFloat("Methyl32", 0.0);
}
//--------------------------------------------------
// section sample
//--------------------------------------------------
if (section == "sample")
{
defaults.setValue("labels", "[Lys8,Arg10]", "Labels used for labelling the sample. [...] specifies the labels for a single sample. For example, [Lys4,Arg6][Lys8,Arg10] describes a mixtures of three samples. One of them unlabelled, one labelled with Lys4 and Arg6 and a third one with Lys8 and Arg10. For permitted labels see \'advanced parameters\', section \'labels\'. If left empty the tool identifies singlets, i.e. acts as peptide feature finder (in this case, 'out_features' must be used for output instead of 'out').");
defaults.setValue("charge", "2:4", "Range of charge states in the sample, i.e. min charge : max charge.");
defaults.setValue("missed_cleavages", 0, "Maximum number of missed cleavages.");
defaults.setMinInt("missed_cleavages", 0);
defaults.setValue("peaks_per_peptide", "3:5", "Range of peaks per peptide in the sample, i.e. min peaks per peptide : max peaks per peptide. For example 3:6, if isotopic peptide patterns in the sample consist of either three, four, five or six isotopic peaks. ", StringList::create("advanced"));
}
//--------------------------------------------------
// section algorithm
//--------------------------------------------------
if (section == "algorithm")
{
defaults.setValue("rt_threshold", 30.0, "Typical retention time [s] over which a characteristic peptide elutes. (This is not an upper bound. Peptides that elute for longer will be reported.)");
defaults.setMinFloat("rt_threshold", 0.0);
defaults.setValue("rt_min", 0.0, "Lower bound for the retention time [s].");
defaults.setMinFloat("rt_min", 0.0);
defaults.setValue("intensity_cutoff", 1000.0, "Lower bound for the intensity of isotopic peaks in a SILAC pattern.");
defaults.setMinFloat("intensity_cutoff", 0.0);
defaults.setValue("intensity_correlation", 0.7, "Lower bound for the Pearson correlation coefficient, which measures how well intensity profiles of different isotopic peaks correlate.");
defaults.setMinFloat("intensity_correlation", 0.0);
defaults.setMaxFloat("intensity_correlation", 1.0);
defaults.setValue("model_deviation", 3.0, "Upper bound on the factor by which the ratios of observed isotopic peaks are allowed to differ from the ratios of the theoretic averagine model, i.e. ( theoretic_ratio / model_deviation ) < observed_ratio < ( theoretic_ratio * model_deviation ).");
defaults.setMinFloat("model_deviation", 1.0);
}
return defaults;
}
