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**ddgraph**: Distinguish direct and indirect interactions with Graphical Modelling**toyExample**: A binary fictional toy example 'DDDataSet' object.

# A binary fictional toy example DDDataSet object.

### Description

`toyExample`

is an example dataset representing a set of 200 fictional cis-regulatory modules (CRMs).
The dataset contains binding patterns for two transcription factors A and B. It is used only in the package
vignette.

### Usage

1 |

### Details

In this fictional dataset we represent binding patterns of two transcription factors A and B on a set of CRMs. The target variable (T) is another binary vector that represents if a CRM is tissue specific or not (as obtained by e.g. transgenic reporter assays).

For more information and detailed examples see the package vignette.

### Examples

1 2 |

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- activePaths: Find all active paths in a (partially) directed graph...
- adjC-dot-allVarInx: Get all the variable indicies in adjC, both target and...
- adjC-dot-allVarNames: Get all the variable names in adjC, both target and...
- adjC-dot-condSetSize: Returns the total size of conditioning set for adjC (i...
- adjC-dot-targetInx: Get all the targetInx values in adjC...
- adjC-dot-toIDs: Make a list of conditional independence tests and converts...
- biased-dot-bn-dot-fit: Random network with a biased degree distribution
- biased-dot-graph: Generate random network with degree distribution
- blockingNodes: Find all such nodes in neighbourhood of source node that are...
- blockingVariables: Version of blockingNodes() for DDGraphs...
- calcDependence: Dependence with target variable
- calculateNCPCRobustnessStats: Calculate NCPCRobustness statistics...
- chisq-dot-val: Get the value of chi-square statistics...
- ciTest-comma-DDDataSet-dash-method: Do conditional independence test on DDDataSet...
- CITestResult-dash-class: Data class to store the results of a conditional independence...
- CITestResultID: Provide a unique ID composing of target, source and...
- CITestResultVar: Return a string representation of a variable represented with...
- classLabels-comma-FurlongDataSet-dash-method: Class labels
- color-dot-legend-dot-DDGraph: Plot color coding legend
- combinationsTest: Significant combinations of variables
- convertPvalueToColorIndex: Convert P-values to color index...
- convertToFactor: Convert data to factor representation
- customPlotPCAlgo: Custom plotting for pcalgo
- datasetName-comma-DDDataSet-dash-method: Dataset name...
- dataType-comma-DDDataSet-dash-method: Return data type
- DDDataSet-dash-class: Dataset class for Direct Dependence Graphs...
- DDGraph-dash-class: Direct Dependence Graph class...
- DDGraphEdge-dash-class: An edge in an DDGraph...
- ddgraph-package: ddgraph package overview
- entropyFromFreq: Calculate entropy from frequencies of observations for...
- estimateNetworkDistribution: Estimate network distribution parameters
- extractCITestResultProperty: Extract CITestResult properties
- extract-dot-targetInx: Extract all values of targetInx from a list of...
- foldChangeFromFreq: Calculate the fold change when x is of size two (always show...
- formulaFalseNeg: Generate class labels by a noisy formula with high false...
- FurlongDataSet-dash-class: Data class for the Furlong dataset...
- graph-dot-to-dot-bn: Convert graphNEL and friends representation to bn...
- independent-dot-contributions-dot-formula: Generate class labels by independent contributions of two...
- independent-dot-contributions-dot-formula-dot-mul: Generate class labels by independent contributions of two...
- initialize-comma-DDDataSet-dash-method: Construct new DDDataSet object...
- initialize-comma-DDGraph-dash-method: Construct new DDGraph object...
- is-dot-binary: Check if data structure has binary data in it
- logseq: Generate sequence in log scale
- loocv: Leave-one-out cross validation
- makeDDDataSet: Construct an DDDataSet object...
- makeNCPCRobustness: Make a new NCPCRobustness object...
- mapEnrichmentToColors: Map enrichment values to colors...
- mapEnrichmentToColorsDual: Map enrichment values into two different palettes for...
- mcMITest: Wrapper around the bnlearn mc-x2 test
- mcX2CLoop: the inner loop for myX2c is implemented in C...
- mcX2Test: Wrapper around the bnlearn mc-x2 test
- mcX2TestB50k: Wrapper around the bnlearn mc-x2 test (B=50k)
- mesoBin: A list of binary 'DDDataSet' objects.
- mesoCont: A list of continuous 'DDDataSet' objects.
- myX2c: The Monte-Carlo chi-square test...
- names-comma-CITestResult-dash-method: Names of slots that can be accessed with $ notation...
- names-comma-DDDataSet-dash-method: Names of variables (+class)
- names-comma-DDGraph-dash-method: Names of properties
- names-comma-FurlongDataSet-dash-method: Names of variables
- ncpc: Make a Direct Dependence Graph using the NCPC algorithm...
- ncpcResampling: NCPC Robustness from resampling
- NCPCRobustness-dash-class: NCPC resampling robustness...
- operators-dash-CITestResult: Access slots using the dollar notation...
- operators-dash-DDDataSet: access a specific variable in the dataset by name...
- operators-dash-DDGraph: access a property by name...
- pcalgMB: Find the markov blanket for the PC algorithm output...
- pcalgNBR: Find the neighbourhood for the PC algorithm output...
- plotBNLearn: A custom plotting function for the BNlearn graphs...
- plot-comma-DDGraph-comma-missing-dash-method: Plot DDGraphs using RGraphviz...
- plotPCalg: Plot the network inferred by the PC algorithm
- plotSVMPerformance: Plot SVM performance into a pdf file
- predSVM: Calculate the decision value of an SVM model
- prob-dot-distr-dot-norm: Normal distribution function for 'random.bn.fit'
- prob-dot-distr-dot-unif: Uniform distribution for 'random.bn.fit'
- pValueAfterMultipleTesting: Multiple testing correction procedure for ncpc()
- random-dot-bn-dot-fit: Generate a random 'bn.fit' network
- rawData-comma-DDDataSet-dash-method: Raw data.frame with data
- readFurlongData: Read the Furlong Dataset
- recalculateSVMparams: Calculate SVM hyperparameters based on grid search
- show-comma-CITestResult-dash-method: show method for CITestResult...
- show-comma-DDDataSet-dash-method: show method for DDDataSet...
- show-comma-DDGraph-dash-method: show method for DDGraph...
- show-comma-DDGraphEdge-dash-method: show method for DDGraphEdge...
- signalMatrix-comma-FurlongDataSet-dash-method: Raw values
- svmFeatureSelectionLOOCV: Nested variable selection using LOOCV
- toDDDataSet-comma-FurlongDataSet-dash-method: DDDataSet object from FurlongDataSet
- toyExample: A binary fictional toy example 'DDDataSet' object.
- variableNames-comma-DDDataSet-dash-method: Names of variables (-class)