<?xml version="1.0" encoding="utf-8"?>
<doc>
<assembly><name>ProteomIQon</name></assembly>
<members>
<member name="M:Deedle.Frame.expandRowsByColumn``4(``0,Microsoft.FSharp.Core.FSharpFunc{``1,Microsoft.FSharp.Core.FSharpFunc{``2,System.Collections.Generic.IEnumerable{``3}}},Deedle.Frame{``1,``0})">
<summary>
 Creates a Frame where each row is mapped to multiple rows based on the input function. The input function takes the rowkey and the value of the given column at this rowkey and returns new keys.
</summary>
</member>
<member name="M:Deedle.Frame.expandRowsByKey``3(Microsoft.FSharp.Core.FSharpFunc{``0,System.Collections.Generic.IEnumerable{``1}},Deedle.Frame{``0,``2})">
<summary>
 Creates a Frame where each row is mapped to multiple rows based on the input function.
</summary>
</member>
<member name="M:Deedle.Frame.dropEmptyCols``2(Deedle.Frame{``0,``1})">
<summary>
 Creates a new data frame that contains only those columns of the original 
 data frame which contain at least one value.
</summary>
</member>
<member name="M:Deedle.Frame.dropEmptyRows``2(Deedle.Frame{``0,``1})">
<summary>
 Creates a new data frame that contains only those columns of the original 
 data frame which contain at least one value.
</summary>
</member>
<member name="M:Deedle.Frame.filterValues``3(Microsoft.FSharp.Core.FSharpFunc{``0,System.Boolean},Deedle.Frame{``1,``2})">
<summary>
 If the predicate returns false for a value, replaces the value with missing
</summary>
</member>
<member name="M:Deedle.Frame.filter``3(Microsoft.FSharp.Core.FSharpFunc{``0,Microsoft.FSharp.Core.FSharpFunc{``1,Microsoft.FSharp.Core.FSharpFunc{``2,System.Boolean}}},Deedle.Frame{``0,``1})">
<summary>
 If the predicate returns false for a value, replaces the value with missing
</summary>
</member>
<member name="M:Deedle.Frame.columnOfRowKeys``2(``0,Deedle.Frame{``1,``0})">
<summary>
 Adds the rowKeys as a new column to the frame
</summary>
</member>
<member name="M:Deedle.Frame.columnOfRowKeysBy``3(``0,Microsoft.FSharp.Core.FSharpFunc{``1,``2},Deedle.Frame{``1,``0})">
<summary>
 Applies the function f to the rowKeys of the frame and adds the result as a new column to the frame
</summary>
</member>
<member name="M:Deedle.Frame.align``4(Microsoft.FSharp.Core.FSharpFunc{``0,``1},Microsoft.FSharp.Core.FSharpFunc{``2,``1},Deedle.Frame{``0,``3},Deedle.Frame{``2,``3})">
<summary>
 Align two data frames by a shared key received through mapping functions. 

 The columns of the joined frames must not overlap and their rows are aligned and multiplied
 by the shared key. The keyFuncs are used to map the rowKeys of the two frames to a shared key. 
 The resulting keys will result from the intersection of the shared Keys.

 The key of the resulting frame will be a triplet of shared key and the two input keys.
</summary>
</member>
<member name="M:Deedle.Frame.createExpandTransformation``2(Microsoft.FSharp.Core.FSharpFunc{``0,System.Collections.Generic.IEnumerable{``1}},Deedle.Indices.IIndex{``0},Deedle.Vectors.VectorConstruction)">
<summary>
 Create transformation on indices/vectors representing the expand operation
</summary>
</member>
<member name="M:Deedle.Frame.createAlignTransformation``3(Microsoft.FSharp.Core.FSharpFunc{``0,``1},Microsoft.FSharp.Core.FSharpFunc{``2,``1},Deedle.Indices.IIndex{``0},Deedle.Indices.IIndex{``2},Deedle.Vectors.VectorConstruction,Deedle.Vectors.VectorConstruction)">
<summary>
 Create transformation on indices/vectors representing the align operation
</summary>
</member>
<member name="M:Deedle.Frame.combineIndexBy``3(Microsoft.FSharp.Core.FSharpFunc{``0,``1},Microsoft.FSharp.Core.FSharpFunc{``2,``1},Deedle.Indices.IIndex{``0},Deedle.Indices.IIndex{``2})">
<summary>
Returns all possible combinations of second and first frame keys sharing the same keyfunction result
</summary>
</member>
<member name="M:Deedle.Frame.reindexBy``2(Microsoft.FSharp.Core.FSharpFunc{``0,``1},Deedle.Indices.IIndex{``0},Deedle.Indices.IIndex{``1},Deedle.Vectors.VectorConstruction)">
<summary>
 Reorder elements in the index to match with another index ordering after applying the given function to the first index
</summary>
</member>
<member name="P:Deedle.Frame.atMostOne">
<summary>
 A generic transformation that works when at most one value is defined
</summary>
</member>
<member name="T:ProteomIQon.Ontologies.SampleProcessing.EnzymeDigestion">
<summary>
 Combine this with the used enzyme
</summary>
</member>
<member name="M:ProteomIQon.FDRControl'.initCalculateLin``1(NLog.Logger,System.Double,Microsoft.FSharp.Core.FSharpFunc{``0,System.Boolean},Microsoft.FSharp.Core.FSharpFunc{``0,System.Double},Microsoft.FSharp.Core.FSharpFunc{``0,System.Double},``0[])">
<summary>
 Calculates monotonized PEP values for a target/decoy dataset based on the decoy/target ratio. Entries are binned with a given bandwidth as intital estiamtor based on the scores. 
 Returns a function which maps from score to PEP value based on a fit of a linear function using linear regression. The linear regression is performed on the logit transformed 
 pep values. The fit focuses on the pep values centered aound the middle of the score distribution
</summary>
</member>
<member name="M:ProteomIQon.FDRControl'.logitTransformPepValues``1(``0[],System.Double[])">
<summary>
 Logit transforms pep values (log10)
</summary>
</member>
<member name="M:ProteomIQon.FDRControl'.calculatePEPValues``1(Microsoft.FSharp.Core.FSharpFunc{``0,System.Double},Microsoft.FSharp.Core.FSharpFunc{``0,System.Double},Microsoft.FSharp.Core.FSharpFunc{``0,System.Double},``0[])">
<summary>
 Calculates the PEP value based on the ratio of Decoys to targets at a given score
</summary>
</member>
<member name="M:ProteomIQon.FDRControl'.createTargetDecoyHis``1(System.Double,Microsoft.FSharp.Core.FSharpFunc{``0,System.Boolean},Microsoft.FSharp.Core.FSharpFunc{``0,System.Double},Microsoft.FSharp.Core.FSharpFunc{``0,System.Double},``0[])">
<summary>
 Creates a Histogram based on a given score of a target/decoy dataset. Each bin contains the information of the total count, the decoy count and the median score.
 (Bin, Count, DecoyCount, Median Score)
</summary>
</member>
<member name="M:ProteomIQon.FDRControl'.calculateQValueStorey``1(``0[],Microsoft.FSharp.Core.FSharpFunc{``0,System.Boolean},Microsoft.FSharp.Core.FSharpFunc{``0,System.Double},Microsoft.FSharp.Core.FSharpFunc{``0,System.Double})">
<summary>
 Gives a function to calculate the q value for a score in a dataset using Storeys method
</summary>
</member>
<member name="M:ProteomIQon.FDRControl'.calculateQValueLogReg``1(System.Double,System.Double,``0[],Microsoft.FSharp.Core.FSharpFunc{``0,System.Boolean},Microsoft.FSharp.Core.FSharpFunc{``0,System.Double},Microsoft.FSharp.Core.FSharpFunc{``0,System.Double})">
<summary>
 Gives a function to calculate the q value for a score in a dataset using Lukas method and Levenberg Marguardt fitting
</summary>
</member>
<member name="M:ProteomIQon.FDRControl'.calculateFDRwithDecoyTargetRatio(ProteomIQon.ProteinInference'.InferredProteinClassItemScored[])">
<summary>
 Calculates Decoy/Target ratio
</summary>
</member>
<member name="M:ProteomIQon.FDRControl'.calculateFDRwithMAYU(ProteomIQon.ProteinInference'.InferredProteinClassItemScored[],System.Tuple{System.String,System.String}[])">
<summary>
 Calculates the fdr of the data using the MAYU method. The proteinsFromDB is the DB that was used for the inference.
</summary>
</member>
<member name="M:ProteomIQon.FDRControl'.expectedFP(ProteomIQon.ProteinInference'.InferredProteinClassItemScored[])">
<summary>
 Calculates the expected false positives for every protein bin and sums them up.
</summary>
</member>
<member name="M:ProteomIQon.FDRControl'.binProteinsLength(ProteomIQon.ProteinInference'.InferredProteinClassItemScored[],System.Tuple{System.String,System.String}[],System.Double)">
<summary>
 Returns proteins sorted into bins according to their size.
 proteins are the proteins which were found in either the reverse or forward proteininference, proteinsFromDB are the proteins with peptide sequence
 on which the inference was performed.
</summary>
</member>
<member name="M:ProteomIQon.FDRControl'.estimatePi0HG(System.Double,System.Double,System.Double)">
<summary>
 Estimates the false positives given the total number of entries, the number of target hits and the number of decoy hits
</summary>
</member>
<member name="M:ProteomIQon.FDRControl'.binningFunction``1(System.Double,System.Double,Microsoft.FSharp.Core.FSharpFunc{``0,System.Double},Microsoft.FSharp.Core.FSharpFunc{``0,System.Boolean},``0[])">
<summary>
 returns scores, pep, q
</summary>
</member>
<member name="M:ProteomIQon.FDRControl'.getLogisticRegressionFunction(FSharp.Stats.Vector{System.Double},FSharp.Stats.Vector{System.Double},System.Double)">
<summary>
 for given data, creates a logistic regression model and returns a mapping function for this model
</summary>
</member>
<member name="T:ProteomIQon.ProteinInference'.QValueInput">
<summary>
 Input for QValue calulation
</summary>
</member>
<member name="T:ProteomIQon.ProteinInference'.InferredProteinClassItemOut">
<summary>
 For a group of proteins, contains information about all peptides that are put into the output file.
</summary>
</member>
<member name="T:ProteomIQon.ProteinInference'.InferredProteinClassItemQValue">
<summary>
 For a group of proteins, contains information about all peptides that might be used for its quantification and score / q-value calculated for it.
</summary>
</member>
<member name="T:ProteomIQon.ProteinInference'.InferredProteinClassItemScored">
<summary>
 For a group of proteins, contains information about all peptides that might be used for its quantification and score calculated for it.
</summary>
</member>
<member name="M:ProteomIQon.ProteinInference'.assignDecoyScoreToTargetScore(System.String,Microsoft.FSharp.Collections.FSharpMap{System.String,System.Tuple{System.Double,System.String[]}})">
<summary>
 Looks if the given protein accession is present in a map of identified decoy proteins and assigns its score when found.
</summary>
</member>
<member name="M:ProteomIQon.ProteinInference'.assignPeptideScores(System.String[],Microsoft.FSharp.Collections.FSharpMap{System.String,System.Double})">
<summary>
 Sums up score of all peptide sequences
</summary>
</member>
<member name="M:ProteomIQon.ProteinInference'.createPeptideProteinRelation``4(System.Collections.Generic.IEnumerable{Microsoft.FSharp.Core.FSharpOption{BioFSharp.PeptideClassification.ProteinModel{``0,``1,``2,Microsoft.FSharp.Collections.FSharpList{``3}}}})">
<summary>
 Creates a lookup data base to assign peptides to the proteins they are contained in
</summary>
</member>
<member name="M:ProteomIQon.ProteinInference'.assignTranscriptsToGenes``1(Microsoft.FSharp.Core.FSharpFunc{System.String,Microsoft.FSharp.Core.FSharpOption{``0}},System.Collections.Generic.IEnumerable{BioFSharp.IO.GFF3.GFFLine{System.Collections.Generic.IEnumerable{System.Char}}})">
<summary>
 By reading GFF creates the protein models (relationships of proteins to each other) which basically means grouping the rnas over the gene loci
 TODO: Don&apos;t group over order but rather group over id
</summary>
</member>
<member name="M:ProteomIQon.ProteinInference'.createProteinModelInfoFromEntry(System.Int32,System.String,BioFSharp.IO.GFF3.GFFEntry)">
<summary>
 Reads geographical information about protein from gff entry and builds the modelinfo of it
 This function takes an RNA gff3 entry and therefore will contain the splice variant id of the gene in its result.
 This splice variant id should be the same in the given FastA-file.
</summary>
</member>
<member name="M:ProteomIQon.ProteinInference'.isRNA(BioFSharp.IO.GFF3.GFFLine{System.Collections.Generic.IEnumerable{System.Char}})">
<summary>
checks if GFF line describes rna
</summary>
</member>
<member name="M:ProteomIQon.ProteinInference'.isGene(BioFSharp.IO.GFF3.GFFLine{System.Collections.Generic.IEnumerable{System.Char}})">
<summary>
checks if GFF line describes gene
</summary>
</member>
<member name="M:ProteomIQon.ProteinInference'.createScoreTargetDecoyCount(System.Double,System.Double,System.Double)">
<summary>
 Gives the decoy and target count at a specific score
</summary>
</member>
<member name="M:ProteomIQon.SearchDB'.getThreadSafePeptideLookUpFromFileBySequenceAndGMod(System.Data.SQLite.SQLiteConnection,BioFSharp.Mz.SearchDB.SearchDbParams)">
<summary>
 Returns a LookUpResult list
</summary>
</member>
<member name="M:ProteomIQon.SearchDB'.getSDBParams(System.Data.SQLite.SQLiteConnection)">
<summary>
 Returns SearchDbParams of a existing database by filePath
</summary>
</member>
<member name="M:ProteomIQon.SearchDB'.selectProteins(System.Data.SQLite.SQLiteConnection)">
<summary>
 Returns Accession and Sequence of Proteins from SearchDB
</summary>
</member>
<member name="M:ProteomIQon.SearchDB'.getProteinPeptideLookUpFromFileBy(System.Data.SQLite.SQLiteConnection)">
<summary>
 Prepares a function which returns a list of protein Accessions tupled with the peptide sequence whose ID they were retrieved by
</summary>
</member>
<member name="M:ProteomIQon.SearchDB'.DB'.SQLiteQuery'.prepareSelectModsequenceBySequenceAndGMod(System.Data.SQLite.SQLiteConnection)">
<summary>
 Prepares statement to select a ModSequence entry by ModSequenceID
</summary>
</member>
<member name="M:ProteomIQon.SearchDB'.DB'.SQLiteQuery'.prepareSelectMassByModSequenceAndGlobalMod(System.Data.SQLite.SQLiteConnection)">
<summary>
 Prepares statement to select a ModSequence entry by Massrange (Between selected Mass -/+ the selected toleranceWidth)
</summary>
</member>
<member name="M:ProteomIQon.SearchDB'.DB'.SQLiteQuery'.prepareSelectPepSequenceByPepSequenceID(System.Data.SQLite.SQLiteConnection,System.Data.SQLite.SQLiteTransaction)">
<summary>
 Prepares statement to select a Peptide Sequence entry by ID
</summary>
</member>
<member name="M:ProteomIQon.SearchDB'.DB'.SQLiteQuery'.prepareSelectProteinAccessionByID(System.Data.SQLite.SQLiteConnection,System.Data.SQLite.SQLiteTransaction)">
<summary>
 Prepares statement to select a Protein Accession entry by ID
</summary>
</member>
<member name="M:ProteomIQon.Fitting'.NonLinearRegression'.LevenbergMarquardtConstrained'.estimatedParamsWithRSS(FSharp.Stats.Fitting.NonLinearRegression.Model,FSharp.Stats.Fitting.NonLinearRegression.SolverOptions,System.Double,System.Double,FSharp.Stats.Vector{System.Double},FSharp.Stats.Vector{System.Double},System.Double[],System.Double[])">
<summary>
 Returns a parameter vector tupled with its residual sum of squares (RSS) as a possible solution for linear least square based nonlinear fitting of a given dataset (xData, yData) with a given
 model function.
</summary>
</member>
<member name="M:ProteomIQon.Fitting'.NonLinearRegression'.LevenbergMarquardtConstrained'.initialParamsOverRangeMidAndSteepness(System.Double[],System.Double[],System.Double[],Microsoft.FSharp.Core.FSharpOption{System.Double})">
<summary>
 Returns an estimate for an initial parameter for the linear least square estimator for a given dataset (xData, yData).
 The steepness and midpoint ranges are given as an array and not estimated. An initial estimate is returned for every given steepness and midpoint in the input array.
 The initial estimation is intended for a logistic function with variable position on the y-axis.
</summary>
</member>
<member name="M:ProteomIQon.Fitting'.NonLinearRegression'.LevenbergMarquardtConstrained'.initialParamsOverRange(System.Double[],System.Double[],System.Double[])">
<summary>
 Returns an estimate for an initial parameter for the linear least square estimator for a given dataset (xData, yData).
 The steepness is given as an array and not estimated. An initial estimate is returned for every given steepness.
 The initial estimation is intended for a logistic function.
</summary>
</member>
<member name="M:ProteomIQon.Fitting'.NonLinearRegression'.LevenbergMarquardtConstrained'.initialParam(System.Double[],System.Double[])">
<summary>
 Returns an estimate for an initial parameter for the linear least square estimator for a given dataset (xData, yData).
 The initial estimation is intended for a logistic function.
</summary>
</member>
<member name="P:ProteomIQon.Fitting'.NonLinearRegression'.LevenbergMarquardtConstrained'.LogisticFunction">
<summary>
 Logistic Function
 Line model of the form &quot;y = a * x + b&quot;
</summary>
</member>
<member name="M:ProteomIQon.SeqIO'.stringFunction``1(System.String,System.Boolean,``0)">
<summary>
Returns a function to format a given value as string
</summary>
</member>
<member name="M:ProteomIQon.DTW'.bestPath(FSharp.Stats.Matrix{System.Double})">
<summary>
 Returns the best warping path.
</summary>
</member>
<member name="M:ProteomIQon.DTW'.warp(Microsoft.FSharp.Core.FSharpOption{System.Int32},Microsoft.FSharp.Core.FSharpOption{System.Double},Microsoft.FSharp.Core.FSharpOption{System.Double},Microsoft.FSharp.Core.FSharpOption{System.Int32},Microsoft.FSharp.Core.FSharpOption{System.Double},Microsoft.FSharp.Core.FSharpOption{System.Int32},System.Double[],System.Double[])">
<summary>
Dynamic Time Warping.
The full matrix of all warping paths is build.
x: First sequence
y: Second sequence
returns: (DTW distance, DTW matrix)
</summary>
</member>
<member name="P:ProteomIQon.Domain.AndromedaParams.PMinPMax">
<summary>
 selects the minimum and maximum amount of peaks retained in a 100 Da window, all combinations are tested and the best result is kept.
</summary>
</member>
<member name="P:ProteomIQon.Domain.WaveletPeakPickingParams.NumberOfScales">
<summary>
 Centroidization
</summary>
</member>
<member name="T:ProteomIQon.Dto.ProteinInferenceResult">
<summary>
 For a group of proteins, contains information about all peptides that are put into the output file.
</summary>
</member>
<member name="M:ProteomIQon.Dto.QuantificationResultModule.tryTargetGetScanTime(ProteomIQon.Dto.QuantificationResult)">
<summary>
 Retrieves the scan time based on the fitted parameter values (HULQ output).
</summary>
</member>
<member name="M:ProteomIQon.Dto.QuantificationResultModule.getTargetScanTimeDifference(ProteomIQon.Dto.QuantificationResult)">
<summary>
 Retrieves the scan time based on the fitted parameter values (HULQ output).
</summary>
</member>
<member name="M:ProteomIQon.Dto.QuantificationResultModule.getTargetStabw(ProteomIQon.Dto.QuantificationResult)">
<summary>
 Retrieves the scan time based on the fitted parameter values (HULQ output).
</summary>
</member>
<member name="M:ProteomIQon.Dto.QuantificationResultModule.getTargetScanTime(ProteomIQon.Dto.QuantificationResult)">
<summary>
 Retrieves the scan time based on the fitted parameter values (HULQ output).
</summary>
</member>
<member name="M:ProteomIQon.Dto.QuantificationResultModule.getTargetIntensity(ProteomIQon.Dto.QuantificationResult)">
<summary>
 Retrieves the scan time based on the fitted parameter values (HULQ output).
</summary>
</member>
<member name="M:ProteomIQon.Core.MzIO.Reader.openConnection(MzIO.IO.IMzIODataReader)">
<summary>
 Opens a connection.
</summary>
</member>
<member name="M:ProteomIQon.Core.MzIO.Reader.beginTransaction(MzIO.IO.IMzIODataReader)">
<summary>
 Initializes a transaction scope.
</summary>
</member>
<member name="M:ProteomIQon.Core.MzIO.Reader.getDefaultRunID(MzIO.IO.IMzIODataReader)">
<summary>
 Returns the default runID used by manufacturers
</summary>
</member>
</members>
</doc>
