ddgraph: Distinguish direct and indirect interactions with Graphical Modelling

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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.

Author
Robert Stojnic
Date of publication
None
Maintainer
Robert Stojnic <robert.stojnic@gmail.com>
License
GPL-3
Version
1.18.0

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