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GeneralWfccmDesign
General WFCCM Design * Wfccm Bug Reports Goals * Version 1 * Generate Scores. * Write basic graphs. * Version 2 * Add Permuatation ...
WfccmAlgorithmFDR
False Discovery Rate Algorithm Calculate adjusted p values using False Discovery Rate Controlling Procedures. FDR Algorithm predefined values: subSize of data ...
WfccmAlgorithmFisher
Fisher Algorithm Performed on a set of non negative numbers and labels of size N. There must be two specific labels. Label 1 must be 1 and label 2 must be 2. There ...
WfccmAlgorithmHu
Hu Algorithm function 1 : log likelihood to estimate logmu * f(logmu) = %$\sum(\frac{1}{2}*logsigma2 \frac{(X exp(logmu))^2}{2*exp(logsigma2)})$% * logsigma2 ...
WfccmAlgorithmInfo
Info Algorithm Performed on an ordered (ascending) set of numbers and labels of size N. There must be only 2 unique labels (Label 1 and label 2). Seperate the list ...
WfccmAlgorithmKS
Kolmogorov Smirnov Algorithm Computes the difference of the distributions of two empirical observation sets. K S Statistic 1 %$N_1$% is the size of group 1 ...
WfccmAlgorithmLikelihoodRatio
Likelihood Ratio Algorithm Suppose that we have data from stratum 0 and stratum 1. The test statistic is computed as : %$Z = 2Nlog(\frac{T}{N}) 2\sum N_jlog(\frac ...
WfccmAlgorithmLogRankWilcoxon
Log Rank and Wilcoxon Algorithm These tests are for comparison of two or more strata of survival data. Suppose that we have data from stratum 0 and stratum 1. Denote ...
WfccmAlgorithmSAM
SAM Algorithm The data is %$x_{ij}$%, i = 1, 2, ... p genes, j = 1, 2, ... n samples, and response data %$y_j$%, j = 1,2, ... n (%$y_j$% may be a vector). Generic ...
WfccmAlgorithmTTest
TTest Algorithm Performed on a set of non negative numbers and labels of size N. There must be two specific labels. Label 1 must be 1 and label 2 must be 2. There ...
WfccmAlgorithmWGA
WGA Algorithm WGA = \begin{displaymath} \frac{d_b}{k_1d_{1} k_2d_{2} \alpha} \end{displaymath} * description of letters * %$n_i$% is the total number of ...
WfccmAlgorithmWilcoxon
Wilcoxon Algorithm Performed on a set of numbers and labels of size N. There must be two specific labels. Label 1 must be 1 and label 2 must be 2. There can also be ...
WfccmBallGraphPanel
ClassBallGraphPanel Public Data Members * int tickMax – Max value of tick of scale, default is 0 * int tickMin – minimum value of tick of scale, default is ...
WfccmBallGraphSummary
BallGraphSummary Public Data Member * ArrayList lines the container for the lines * string title title of the graph * string testLabel1 label of testing ...
WfccmChartPanel
ChartPanel Public Methods * saveImage(String imgName) saves image of the chart (as a PNG file) to the given image name * setDimensions(float top, bottom, ...
WfccmCluster
Cluster Parent: DataSet Public Methods * Cluster public constructor * Copy used to copy an instance of a cluster * SetMatric (char,char,char) ...
WfccmClusterNode
ClusterNode Enumeration NodeType * Node * Gene * Array Static (Class) Methods * ClusterNode Compare3(ClusterNode, ClusterNode, ClusterNode, bool) ...
WfccmClusterSummary
ClusterSummary NameRank Class * name * rank Public Methods * Load(string) Loads the given CDT file * string GetArryNameByRank(name, rank) given ...
WfccmCombinationManager
CombinationManager Public Methods * SetBases(ArrayList of int) Sets the sizes of the bases. * Arraylist GetCombination(int) Returns the 0 base indices that ...
WfccmCriteria
Criteria Public Members * Property Name * Property Operator * Property Value * Property IgnoreNumPass Protected * string name Name of the ...
WfccmCriteriaManager
CriteriaManager Public Methods * CriteriaManager(CriteriaManager) The copy constructor. * Remove(string, string, double) Removes a score name, operator ...
WfccmCriteriaManagerPanel
CriteriaManagerPanel Public Methods * loadCM(CriteriaManager, ArrayList, bool) Takes the CriteriaManager to load, a list of score names, and whether or not the ...
WfccmCriteriaManagerWarning
CriteriaManagerWarning Confirms changing the CriteriaManager type on the CriteriaManagerPanel because all criteria and the STD function are removed.
WfccmCriteriaSet
CriteriaSet Public Methods * Property Pass * Property NumPass The number of rows that passed the evaluation. If IgnoreNumPass then don't count. * SetColumnValue ...
WfccmCutoffManager
CutoffManager Parent: CriteriaManager Public Methods * CutoffManager(CutoffManager) The copy constructor. * Add(string, string, double) Adds a score name ...
WfccmDataContainer
DataContainer Public Methods * DataContainer(DataContainer) Copy constructer. * AddColumn(string) Appends a new column of data, sets the name, and returns ...
WfccmDataGrouping
DataGrouping Public Methods * DataGrouping(DataGrouping) Copy constructor. * Add(string, string) Adds a Column by name and sets group descriptor (defaults ...
WfccmDataGroupingPanel
DataGroupingPanel Public Methods * loadDG(DataSetInfo, DataGrouping, bool, bool) Takes the data information, the grouping to load, and whether the grouping is ...
WfccmDataSet
DataSet Parent: DataContainer, Interface: IDataSet Public Methods * DataSet(DataSet) Copy Constructor overload that handles the name list. * SetDataPoint ...
WfccmDataSetPanel
DataSetPanel Public Methods * LoadDataSetPanel(DataSetInfo) loads the DataSet contained within the DataSetInfo object. If an InformationSet has also been assigned ...
WfccmDistance
Distance Public Methods * DistanceResult DoDistance(DataSet, DataGrouping, FilteredScore) Runs distance on the provided traning dataset. * DistanceResult ...
WfccmDistanceOutput
DistanceOutput Public Methods * DistanceOutput() * DistanceOutput(DistanceOutput) Copy Constructor * DistanceColumn GetByColName(string name) returns ...
WfccmDistancePanel
DistancePanel Public Methods * LoadDistancePanel(TreeView) Loads the control with the CriteriaManagers, training groups, testing data, and testing groups for ...
WfccmDistanceReport
DistanceReport Static Methods * WriteMissedColumn(ArrayList, string, bool, double) Will first filter distanceResults for runs where overall percent correct ...
WfccmDistanceResult
DistanceResult Public Members * FilteredScores List of ids, numPass and the modifiers. * CriteriaSet criteria * DistanceOutput train * DistanceOutput ...
WfccmExpression
Expression Public Methods * Expression(string) Creation constructor. Sets function to the passed string, checks the validity of the function and converts to ...
WfccmFilteredScore
FilteredScore Parent: Score Public Methods * FilteredScore(Score, CriteriaSet) Filters a score according to the criteria set. Creates the numPass column. ...
WfccmIDataSet
IDataSet Public Methods * GetDataPoint(int, int) * GetColumnName(int) * GetColIndexFromName(string) * GetRowId(int) * GetRowIndexFromId(int) * GetRowName ...
WfccmInformationSet
InformationSet Parent: DataContainer Public * SetDataPoint(int, int, string) Set the data at that point. * GetDataPoint(int, int) Gets the data at that ...
WfccmMemoryMapDataSet
MemoryMapDataSet Interface: IDataSet Public Methods * MemoryMapDataSet(string) Constructor that takes the path/file name. * MemoryMapDataSet(string, int) ...
WfccmMissedChart
MissedChart Public Methods * MissedChart(MissedValues) creates a new missed chart to visualize the given object (can be null) Properties * InfoSet The ...
WfccmMissedValues
MissedValues Note: This class's structure is dependent entirely on DistanceReport.WriteMissedColumn() function Public Members * highlightRuns Arraylist of highlighted ...
WfccmNetwork
Network Public Methods * Network(IPAddress, int) Constructor for starting a connection. * Network(string, int) Constructor for starting a connection. ...
WfccmNetworkListener
NetworkListener Public Methods * NetworkListener(int) The constructor. * Start() Starts listening for incoming connections. * Stop() Stops listening ...
WfccmOptionData
OptionData Public Methods * OptionData() * OptionData(string) * Copy() * Load(string) * Save(string) Properties * AutoLoadLog * AutoLoadInfo ...
WfccmPartitionedDataSet
PartitionedDataSet Public Methods * PartitionedDataSet(string) Constructor that takes the path to the DataSet. * PartitionedDataSet(string, int) Constructor ...
WfccmProjectData
ProjectData Public * Collection of DataSetInfo * string working directory * class DataSetInfo * path for data set * path for score set ...
WfccmQcAgreement
Kappa Value and Agreement Rate algorithms * 1. For each gene/feature, convert their are values to binary * new value(proteinomic data) = 1 if old value is ...
WfccmQualitycontrol
QualityControl Private Methods * GenerateAgreement_NoGp (DoubleProgress, DataSet, string, string) * GenerateAgreement_InGp (DoubleProgress, DataSet, DataGrouping ...
WfccmRfunctions
Rfunctions Public Methods * Average(ArrayList) Returns the mean. * StDev(ArrayList, double) Returns the standard deviation. * Var(ArrayList) Returns ...
WfccmScore
Score Parent: DataContainer Public Methods * Score() Default Constructor. * Score(Score) Copy Constructor. * Score(string) Loads the Score from ...
WfccmScoreExpression
ScoreExpression Parent: Score Public Methods * GenerateScores(DataSet, DataGrouping) defaults to ignore zeroes * GenerateScores(DataSet, DataGrouping, bool ...
WfccmScoreHu
ScoreHu Public Methods * ScoreHu() Default Constructor. * ScoreHu(ScoreHu) Copy Constructor. * ScoreHu(string) Loads the score from a file. ...
WfccmScorePanel
ScorePanel Public Methods * LoadScore(Score, DataSet, string) * loads the given score, appending the actual row names from the given DataSet to the rowIDs ...
WfccmScoreSam
ScoreSam Parent: Score Public Methods * ScoreSam() the default constructor. * ScoreSam(ScoreSam) copy constructor. * ScoreSam(string) Constructors ...
WfccmScoreTTest
ScoreTTest Parent: Score Public Methods * ScoreTTest() the default constructor. * ScoreTTest(ScoreTTest) copy constructor. * ScoreTTest(string) ...
WfccmSummaryModule
Summary Public Methods * ScoreSummary(ArrayList) Returns an InformationSet that summarizes all of the Scores given. * ScoreSummary(Score, ...) ScoreSummary ...
WfccmSummaryPanel
SummaryPanel Public Methods * SummaryPanel() Default constructor * SummaryPanel(SummaryPercentages) create a new Summary panel with the given percentages ...
WfccmSummaryPercentages
SummaryPercentages Public Members * ArrayList Grp1 Grp2 Pcts Train Test Percentages * ArrayList Train Test Pcts Percentages for training or testing ...
WfccmThreadPool
ThreadPool Public Methods ThreadManager(int, WorkObject ) Remarks * Accepts a set of workobjects and does the work with the number of threads passed. This ...
WfccmTopnManager
TopNManager Parent: CriteriaManager Public Members * TopNManager(TopNManager) The copy constructor. * Add(string, string, double) Adds a score name, operator ...
WfccmWorkObject
WorkObject Public Members * int workObjNum workObject id number. Public Methods * DoWork() the function to run distance Remarks Generic work object ...
WfccmWorkObject_Distance
WorkObject Public Members * CriterialManagemer cm * DataSet ds * DataGrouping dg * Score scr * DataSet tds * DataGrouping tdg Public Methods ...
Number of topics: 64
 
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