Prediction (BioFSharp) | BioFSharp

Prediction Module

Namespace: BioFSharp.ML
Assembly: BioFSharp.ML.dll
Parent Module: DPPOP

Contains functions to execute peptide observability prediction using the deep neural network dppop.

Types

Type	Description
Model	Options concerning the model used for prediction.

Functions and values

Function or value	Description
`scoreBy model distinctPeptideSet data` Full Usage: `scoreBy model distinctPeptideSet data` Parameters: model : `Model` distinctPeptideSet : `Set<string>` data : `PredictionInput[]` Returns: `PredictionOutput[]`	For expert use. Returns the observability prediction for the input peptides. Loads a trained CNTK model (either dppops plant/nonPlant models or a custom model) and evaluates the scores for the given collection of features (PredictionInput) No feature normalization is done. model : `Model` distinctPeptideSet : `Set<string>` data : `PredictionInput[]` Returns: `PredictionOutput[]`
`scoreDppopNonPlant proteome proteinsOfInterest` Full Usage: `scoreDppopNonPlant proteome proteinsOfInterest` Parameters: proteome : `FastaItem<BioArray<AminoAcid>> seq` proteinsOfInterest : `FastaItem<BioArray<AminoAcid>> seq` Returns: `PredictionOutput[] seq`	Returns relative observability scores for uniquely mapping peptides of proteins of interest using dppops non-plant model and feature normalization procedure, given the proteome of the organism. proteome : `FastaItem<BioArray<AminoAcid>> seq` proteinsOfInterest : `FastaItem<BioArray<AminoAcid>> seq` Returns: `PredictionOutput[] seq`
`scoreDppopPlant proteome proteinsOfInterest` Full Usage: `scoreDppopPlant proteome proteinsOfInterest` Parameters: proteome : `FastaItem<BioArray<AminoAcid>> seq` proteinsOfInterest : `FastaItem<BioArray<AminoAcid>> seq` Returns: `PredictionOutput[] seq`	Returns relative observability scores for uniquely mapping peptides of proteins of interest using dppops plant model and feature normalization procedure, given the proteome of the organism. proteome : `FastaItem<BioArray<AminoAcid>> seq` proteinsOfInterest : `FastaItem<BioArray<AminoAcid>> seq` Returns: `PredictionOutput[] seq`
`scoreProteinsAgainstProteome model featureNormalization proteome proteinsOfInterest` Full Usage: `scoreProteinsAgainstProteome model featureNormalization proteome proteinsOfInterest` Parameters: model : `Model` featureNormalization : `PredictionInput -> PredictionInput` proteome : `FastaItem<BioArray<AminoAcid>> seq` proteinsOfInterest : `FastaItem<BioArray<AminoAcid>> seq` Returns: `PredictionOutput[] seq`	Returns relative observability scores for uniquely mapping peptides of proteins of interest given a model, normalization procedure for features, and the proteome of the organism. model : `Model` featureNormalization : `PredictionInput -> PredictionInput` proteome : `FastaItem<BioArray<AminoAcid>> seq` proteinsOfInterest : `FastaItem<BioArray<AminoAcid>> seq` Returns: `PredictionOutput[] seq`