ddgraph: Distinguish direct and indirect interactions with Graphical Modelling

Distinguish direct from indirect interactions in gene regulation and infer combinatorial code from highly correlated variables such as transcription factor binding profiles. The package implements the Neighbourhood Consistent PC algorithm (NCPC) and draws Direct Dependence Graphs to represent dependence structure around a target variable. The package also provides a unified interface to other Graphical Modelling (Bayesian Network) packages for distinguishing direct and indirect interactions.

AuthorRobert Stojnic
Date of publicationNone
MaintainerRobert Stojnic <robert.stojnic@gmail.com>
LicenseGPL-3
Version1.18.0

View on Bioconductor

Man pages

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)

Files in this package

ddgraph/.Rinstignore
ddgraph/DESCRIPTION
ddgraph/NAMESPACE
ddgraph/R
ddgraph/R/AllClassses.R ddgraph/R/AllGenerics.R ddgraph/R/calcDependence.R ddgraph/R/citest.R ddgraph/R/combinations.R ddgraph/R/dsep.R ddgraph/R/furlong.R ddgraph/R/methods-CITestResult.R ddgraph/R/methods-DDDataSet.R ddgraph/R/methods-DDGraph.R ddgraph/R/methods-DDGraphEdge.R ddgraph/R/misc.R ddgraph/R/ncpc.R ddgraph/R/other-algorithms.R ddgraph/R/plot-colour.R ddgraph/R/plot.R ddgraph/R/randomnet.R ddgraph/R/resampling.R ddgraph/R/svm.R
ddgraph/build
ddgraph/build/vignette.rds
ddgraph/data
ddgraph/data/mesoBin.RData
ddgraph/data/mesoCont.RData
ddgraph/data/toyExample.RData
ddgraph/inst
ddgraph/inst/NEWS
ddgraph/inst/doc
ddgraph/inst/doc/ddgraph.R
ddgraph/inst/doc/ddgraph.Rnw
ddgraph/inst/doc/ddgraph.pdf
ddgraph/inst/extdata
ddgraph/inst/extdata/supplementary_table_8_training_set.txt
ddgraph/inst/tests
ddgraph/inst/tests/gold_standard
ddgraph/inst/tests/gold_standard/meso_0.05.txt
ddgraph/inst/tests/gold_standard/meso_0.1.txt
ddgraph/inst/tests/gold_standard/meso_0.2.txt
ddgraph/inst/tests/gold_standard/meso_sm_0.05.txt
ddgraph/inst/tests/gold_standard/meso_sm_0.1.txt
ddgraph/inst/tests/gold_standard/meso_sm_0.2.txt
ddgraph/inst/tests/gold_standard/sm_0.05.txt
ddgraph/inst/tests/gold_standard/sm_0.1.txt
ddgraph/inst/tests/gold_standard/sm_0.2.txt
ddgraph/inst/tests/gold_standard/star-meso_0.05.txt
ddgraph/inst/tests/gold_standard/star-meso_0.1.txt
ddgraph/inst/tests/gold_standard/star-meso_0.2.txt
ddgraph/inst/tests/gold_standard/star-meso_sm_0.05.txt
ddgraph/inst/tests/gold_standard/star-meso_sm_0.1.txt
ddgraph/inst/tests/gold_standard/star-meso_sm_0.2.txt
ddgraph/inst/tests/gold_standard/star-sm_0.05.txt
ddgraph/inst/tests/gold_standard/star-sm_0.1.txt
ddgraph/inst/tests/gold_standard/star-sm_0.2.txt
ddgraph/inst/tests/gold_standard/star-vm_0.05.txt
ddgraph/inst/tests/gold_standard/star-vm_0.1.txt
ddgraph/inst/tests/gold_standard/star-vm_0.2.txt
ddgraph/inst/tests/gold_standard/star-vm_sm_0.05.txt
ddgraph/inst/tests/gold_standard/star-vm_sm_0.1.txt
ddgraph/inst/tests/gold_standard/star-vm_sm_0.2.txt
ddgraph/inst/tests/gold_standard/vm_0.05.txt
ddgraph/inst/tests/gold_standard/vm_0.1.txt
ddgraph/inst/tests/gold_standard/vm_0.2.txt
ddgraph/inst/tests/gold_standard/vm_sm_0.05.txt
ddgraph/inst/tests/gold_standard/vm_sm_0.1.txt
ddgraph/inst/tests/gold_standard/vm_sm_0.2.txt
ddgraph/inst/tests/reports
ddgraph/inst/tests/reports/this_is_where_test_results_go.txt
ddgraph/inst/tests/test_DDDataSet.R
ddgraph/inst/tests/test_FurlongDataSet.R
ddgraph/inst/tests/test_NCPCRobustness.R
ddgraph/inst/tests/test_functions.R
ddgraph/inst/tests/test_lake.R
ddgraph/man
ddgraph/man/CITestResult-dash-class.Rd ddgraph/man/CITestResultID.Rd ddgraph/man/CITestResultVar.Rd ddgraph/man/DDDataSet-dash-class.Rd ddgraph/man/DDGraph-dash-class.Rd ddgraph/man/DDGraphEdge-dash-class.Rd ddgraph/man/FurlongDataSet-dash-class.Rd ddgraph/man/NCPCRobustness-dash-class.Rd ddgraph/man/activePaths.Rd ddgraph/man/adjC-dot-allVarInx.Rd ddgraph/man/adjC-dot-allVarNames.Rd ddgraph/man/adjC-dot-condSetSize.Rd ddgraph/man/adjC-dot-targetInx.Rd ddgraph/man/adjC-dot-toIDs.Rd ddgraph/man/biased-dot-bn-dot-fit.Rd ddgraph/man/biased-dot-graph.Rd ddgraph/man/blockingNodes.Rd ddgraph/man/blockingVariables.Rd ddgraph/man/calcDependence.Rd ddgraph/man/calculateNCPCRobustnessStats.Rd ddgraph/man/chisq-dot-val.Rd ddgraph/man/ciTest-comma-DDDataSet-dash-method.Rd ddgraph/man/classLabels-comma-FurlongDataSet-dash-method.Rd ddgraph/man/color-dot-legend-dot-DDGraph.Rd ddgraph/man/combinationsTest.Rd ddgraph/man/convertPvalueToColorIndex.Rd ddgraph/man/convertToFactor.Rd ddgraph/man/customPlotPCAlgo.Rd ddgraph/man/dataType-comma-DDDataSet-dash-method.Rd ddgraph/man/datasetName-comma-DDDataSet-dash-method.Rd ddgraph/man/ddgraph-package.Rd ddgraph/man/entropyFromFreq.Rd ddgraph/man/estimateNetworkDistribution.Rd ddgraph/man/extract-dot-targetInx.Rd ddgraph/man/extractCITestResultProperty.Rd ddgraph/man/foldChangeFromFreq.Rd ddgraph/man/formulaFalseNeg.Rd ddgraph/man/graph-dot-to-dot-bn.Rd ddgraph/man/independent-dot-contributions-dot-formula-dot-mul.Rd ddgraph/man/independent-dot-contributions-dot-formula.Rd ddgraph/man/initialize-comma-DDDataSet-dash-method.Rd ddgraph/man/initialize-comma-DDGraph-dash-method.Rd ddgraph/man/is-dot-binary.Rd ddgraph/man/logseq.Rd ddgraph/man/loocv.Rd ddgraph/man/makeDDDataSet.Rd ddgraph/man/makeNCPCRobustness.Rd ddgraph/man/mapEnrichmentToColors.Rd ddgraph/man/mapEnrichmentToColorsDual.Rd ddgraph/man/mcMITest.Rd ddgraph/man/mcX2CLoop.Rd ddgraph/man/mcX2Test.Rd ddgraph/man/mcX2TestB50k.Rd ddgraph/man/mesoBin.Rd ddgraph/man/mesoCont.Rd ddgraph/man/myX2c.Rd ddgraph/man/names-comma-CITestResult-dash-method.Rd ddgraph/man/names-comma-DDDataSet-dash-method.Rd ddgraph/man/names-comma-DDGraph-dash-method.Rd ddgraph/man/names-comma-FurlongDataSet-dash-method.Rd ddgraph/man/ncpc.Rd ddgraph/man/ncpcResampling.Rd ddgraph/man/operators-dash-CITestResult.Rd ddgraph/man/operators-dash-DDDataSet.Rd ddgraph/man/operators-dash-DDGraph.Rd ddgraph/man/pValueAfterMultipleTesting.Rd ddgraph/man/pcalgMB.Rd ddgraph/man/pcalgNBR.Rd ddgraph/man/plot-comma-DDGraph-comma-missing-dash-method.Rd ddgraph/man/plotBNLearn.Rd ddgraph/man/plotPCalg.Rd ddgraph/man/plotSVMPerformance.Rd ddgraph/man/predSVM.Rd ddgraph/man/prob-dot-distr-dot-norm.Rd ddgraph/man/prob-dot-distr-dot-unif.Rd ddgraph/man/random-dot-bn-dot-fit.Rd ddgraph/man/rawData-comma-DDDataSet-dash-method.Rd ddgraph/man/readFurlongData.Rd ddgraph/man/recalculateSVMparams.Rd ddgraph/man/show-comma-CITestResult-dash-method.Rd ddgraph/man/show-comma-DDDataSet-dash-method.Rd ddgraph/man/show-comma-DDGraph-dash-method.Rd ddgraph/man/show-comma-DDGraphEdge-dash-method.Rd ddgraph/man/signalMatrix-comma-FurlongDataSet-dash-method.Rd ddgraph/man/svmFeatureSelectionLOOCV.Rd ddgraph/man/toDDDataSet-comma-FurlongDataSet-dash-method.Rd ddgraph/man/toyExample.Rd ddgraph/man/variableNames-comma-DDDataSet-dash-method.Rd
ddgraph/src
ddgraph/src/Makevars
ddgraph/src/Makevars.win
ddgraph/src/mcX2cloop.cpp
ddgraph/tests
ddgraph/tests/test-all.R
ddgraph/vignettes
ddgraph/vignettes/ddgraph.Rnw
ddgraph/vignettes/references.bib

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