ProteinInferenceOptions_FIDO (BioFSharp.Mz) | BioFSharp.Mz

BioFSharp.Mz

ProteinInferenceOptions_FIDO Type

Namespace: BioFSharp.Mz
Assembly: BioFSharp.Mz.dll
Parent Module: Parameters
Base Type: obj
All Interfaces: IEquatable<ProteinInferenceOptions_FIDO> , IStructuralEquatable , IComparable<ProteinInferenceOptions_FIDO> , IComparable , IStructuralComparable

Union cases

Union case	Description
`Alpha float` Full Usage: `Alpha float` Parameters: Item : `float`	Set Fido's probability with which a present protein emits an associated peptide. Set by grid search if not specified. Item : `float`
`Beta float` Full Usage: `Beta float` Parameters: Item : `float`	Set Fido's probability of creation of a peptide from noise. Set by grid search if not specified. Item : `float`
`EmpricialQValue` Full Usage: `EmpricialQValue`	Estimate empirical p-values and q-values using target-decoy analysis.
`Gamma float` Full Usage: `Gamma float` Parameters: Item : `float`	Set Fido's prior probability that a protein is present in the sample. Set by grid search if not specified. Item : `float`
`GridSearchDepth float` Full Usage: `GridSearchDepth float` Parameters: Item : `float`	Setting the gridsearch-depth to 0 (fastest), 1 or 2 (slowest) controls how much computational time is required for the estimation of alpha, beta and gamma parameters for Fido. Default = 0. Item : `float`
`GridSearchSpeed float` Full Usage: `GridSearchSpeed float` Parameters: Item : `float`	Apply the specified threshold to PSM, peptide and protein probabilities to obtain a faster estimate of the alpha, beta and gamma parameters. Default = 0; Recommended when set = 0.2. Item : `float`
`NoSubgraphSplitting` Full Usage: `NoSubgraphSplitting`	Do not approximate the posterior distribution by allowing large graph components to be split into subgraphs. The splitting is done by duplicating peptides with low probabilities. Splitting continues until the number of possible configurations of each subgraph is below 2^18.
`ProteinTruncationThreshold` Full Usage: `ProteinTruncationThreshold`	To speed up inference, proteins for which none of the associated peptides has a probability exceeding the specified threshold will be assigned probability = 0. Default = 0.01.
`QValueThreshold float` Full Usage: `QValueThreshold float` Parameters: Item : `float`	Q-value threshold that will be used in the computation of the MSE and ROC AUC score in the grid search. Recommended 0.05 for normal size datasets and 0.1 for big size datasets. Default = 0.1. Item : `float`
`UseFido` Full Usage: `UseFido`	Use the Fido algorithm to infer protein probabilities.

Instance members

Instance member	Description
`this.IsAlpha` Full Usage: `this.IsAlpha` Returns: `bool`	Returns: `bool`
`this.IsBeta` Full Usage: `this.IsBeta` Returns: `bool`	Returns: `bool`
`this.IsEmpricialQValue` Full Usage: `this.IsEmpricialQValue` Returns: `bool`	Returns: `bool`
`this.IsGamma` Full Usage: `this.IsGamma` Returns: `bool`	Returns: `bool`
`this.IsGridSearchDepth` Full Usage: `this.IsGridSearchDepth` Returns: `bool`	Returns: `bool`
`this.IsGridSearchSpeed` Full Usage: `this.IsGridSearchSpeed` Returns: `bool`	Returns: `bool`
`this.IsNoSubgraphSplitting` Full Usage: `this.IsNoSubgraphSplitting` Returns: `bool`	Returns: `bool`
`this.IsProteinTruncationThreshold` Full Usage: `this.IsProteinTruncationThreshold` Returns: `bool`	Returns: `bool`
`this.IsQValueThreshold` Full Usage: `this.IsQValueThreshold` Returns: `bool`	Returns: `bool`
`this.IsUseFido` Full Usage: `this.IsUseFido` Returns: `bool`	Returns: `bool`