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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("ddgraph")
AuthorRobert Stojnic
Bioconductor views GraphAndNetwork
Date of publicationNone
MaintainerRobert Stojnic <robert.stojnic@gmail.com>
LicenseGPL-3
Version1.20.0

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)

Functions

[ Man page
activePaths Man page
adjC.allVarInx Man page
adjC.allVarNames Man page
adjC.condSetSize Man page
adjC.targetInx Man page
adjC.toIDs Man page
biased.bn.fit Man page
biased.graph Man page
blockingNodes Man page
blockingVariables Man page
calcDependence Man page
calculateNCPCRobustnessStats Man page
chisq.val Man page
ciTest Man page
ciTest,DDDataSet-method Man page
CITestResult Man page
[[,CITestResult,ANY,ANY-method Man page
CITestResult-class Man page
CITestResultID Man page
[[,CITestResult-method Man page
$,CITestResult-method Man page
$,CITestResult-method Man page
CITestResultVar Man page
classLabels Man page
classLabels,FurlongDataSet-method Man page
color.legend.DDGraph Man page
combinationsTest Man page
convertPvalueToColorIndex Man page
convertToFactor Man page
customPlotPCAlgo Man page
datasetName Man page
datasetName,DDDataSet-method Man page
dataType Man page
dataType,DDDataSet-method Man page
DDDataSet Man page
[,DDDataSet,ANY,ANY,ANY-method Man page
[,DDDataSet,ANY,ANY-method Man page
DDDataSet-class Man page
[,DDDataSet-method Man page
[[,DDDataSet-method Man page
[[,DDDataSet-method Man page
$,DDDataSet-method Man page
$,DDDataSet-method Man page
ddgraph Man page
DDGraph Man page
DDGraph-class Man page
DDGraphEdge Man page
DDGraphEdge-class Man page
$,DDGraph-method Man page
$,DDGraph-method Man page
ddgraph-package Man page
entropyFromFreq Man page
estimateNetworkDistribution Man page
extractCITestResultProperty Man page
extract.targetInx Man page
foldChangeFromFreq Man page
formulaFalseNeg Man page
FurlongDataSet Man page
FurlongDataSet-class Man page
graph.to.bn Man page
independent.contributions.formula Man page
independent.contributions.formula.mul Man page
initialize,DDDataSet-method Man page
initialize,DDGraph-method Man page
is.binary Man page
logseq Man page
loocv Man page
makeDDDataSet Man page
makeNCPCRobustness Man page
mapEnrichmentToColors Man page
mapEnrichmentToColorsDual Man page
mcMITest Man page
mcX2CLoop Man page
mcX2Test Man page
mcX2TestB50k Man page
mesoBin Man page
mesoCont Man page
myX2c Man page
names,CITestResult-method Man page
names,DDDataSet-method Man page
names,DDGraph-method Man page
names,FurlongDataSet-method Man page
ncpc Man page
ncpcResampling Man page
NCPCRobustness Man page
NCPCRobustness-class Man page
pcalgMB Man page
pcalgNBR Man page
plot Man page
plotBNLearn Man page
plot,DDGraph,missing-method Man page
plotPCalg Man page
plotSVMPerformance Man page
predSVM Man page
prob.distr.norm Man page
prob.distr.unif Man page
pValueAfterMultipleTesting Man page
random.bn.fit Man page
rawData Man page
rawData,DDDataSet-method Man page
readFurlongData Man page
recalculateSVMparams Man page
show,CITestResult-method Man page
show,DDDataSet-method Man page
show,DDGraphEdge-method Man page
show,DDGraph-method Man page
signalMatrix Man page
signalMatrix,FurlongDataSet-method Man page
svmFeatureSelectionLOOCV Man page
toDDDataSet Man page
toDDDataSet,FurlongDataSet-method Man page
toyExample Man page
variableNames Man page
variableNames,DDDataSet-method Man page

Files

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

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