API for mzinkgraf/ConsensusCoExpression
What the package does (short line)

Global functions
AddTraitToPCs Source code
AdjacencyMatrix Source code
AdjacencyMatrixR Source code
AverageExprFrame Source code
AverageExprMatrix Source code
AverageModules Source code
BarplotWithTextLabels Source code
BestHeightCut Source code
CausalChildren Source code
CheckSets Source code
ClusterCoef.fun Source code
ColorsFromLabels Source code
ColumnCor Source code
ConsensusCoExpression Man page
ConsensusCoExpression-package Man page
ConsensusDiagnostics Source code
ConsensusModules Source code
ConsensusOrderPCs Source code
ConsensusPCDissimilarity Source code
CoreScatter Source code
CoreSize Source code
CorrelationPreservation Source code
DegreeInOut Source code
DisplayColors Source code
EvaluateClusters Source code
GOLabels Source code
GOanalysis Source code
GOgenes Source code
GetConnectivity Source code
GetModules Source code
GetNetwork Source code
GreenBlackRed Source code
GreenWhiteRed Source code
HeatmapWithTextLabels Source code Source code
HubGeneSignificance Source code
ImputeExprData Source code
IntersectModules Source code
KeepCommonProbes Source code
MergeCloseModules Source code
ModuleEnrichment1 Source code
ModuleNumber Source code
ModulePCs Source code
ModulePrinComps1 Source code
ModulePrincipalComponents Source code
NetworkModulePCs Source code
NetworkScreening1 Source code
NewBranch Source code
NormalizeLabels Source code
OrderNames Source code
OrderPCs Source code
PeakTypeByDiff Source code
PickHardThreshold Source code
PickSoftThreshold Source code
PlotCorMEMsAndDendros Source code
PlotCorPCs Source code
PlotCorPCsAndDendros Source code
PlotCorPCs_1 Source code
PlotExpPCsCor Source code
PowerConnectivities Source code
PrintSpaces Source code
ProbePermutationTest Source code
Rand2 Source code
RedWhiteGreen Source code Source code
ReverseRows Source code Source code
ReverseVector Source code Source code
ScaleFreeAnalysis Source code
ScaleFreePlot1 Source code
SelectGenesByConnectivity Source code
SelectGenesByMinConnectivity Source code
SelectGenesByRestrConnectivity Source code
SelectTraits Source code Source code
SetConsensusModules Source code
SetConsensusModules2 Source code
SetCorrelationPreservation Source code
SignedTOMdist Source code
SizeWindow Source code
SoftConnectivity Source code
StandardScreening1 Source code
TOMdist1 Source code
TOMdistROW Source code
TOMkdist1 Source code
TOMplot1 Source code
TOMplot2 Source code
TrafoCorMatrix Source code
WithinModuleAnalysis1 Source code
WithinModuleCindex1 Source code
accuraciesFnc Source code
addErrorBars.xy Source code
addOrnaments Source code
allocateJobs Source code
alternatingAngles Source code
approx Source code
assignModuleColor Source code
assignModuleNumber Source code
atGO2Potri Source code
atGO2PotriAnno Source code
atGOanalysis Source code
atGOanalysisBP Source code
barplotArray Source code
bicor.original Source code
bicorw Source code
bicov.original Source code
bicovw Source code
brace.horizontal Source code
checkMultiMEMs Source code
checkSets Source code
chiSquare.table Source code
choosenew Source code
circlePlot Source code
collectGarbage Source code
collect_garbage Source code
consensusMEDissimilarity Source code
consensusOrderMEMs Source code
consensusOrderMEs Source code
corMatMat Source code
corMats Source code
corVMat Source code
cutTreeStatic Source code
cutreeDynamic Source code
cutreeDynamic.1 Source code
cutreeDynamicTree Source code
cutreeHybrid Source code
dendrogramOrderings Source code
distributionOnSNPs2 Source code
drawEllipse Source code
drawRectangle Source code
entrez2geneSymbol Source code
eps Source code
err.bp Source code
evalInvDist Source code
extend Source code
fisherPvector Source code
fixDataStructure Source code
fixLabels Source code
grey2red Source code
hclustplot1 Source code
hclustplotn Source code
indentSpaces Source code
initLib Source code
intervalOverlap Source code
invertEmpiricalDistribution Source code
isMultiData Source code
kME Source code
kWithinModule Source code
labelPosition Source code
labeledBarplot2 Source code
labeledBarplotArray Source code
labeledBoxplot Source code
labeledPlot Source code
labels2colors Source code
legendClean Source code
linAge Source code
linDate Source code
linearizeDate Source code
list2multiData Source code
locateCluster Source code
logTrafo Source code
makeCross Source code
matrixPCor Source code
mean1 Source code
meanw Source code
medianw Source code
merge2Clusters Source code
mergeCloseModules Source code
minWhichMin Source code
moduleEigenMatrices Source code
moduleEigengenes Source code
moduleHeatmapAndEigengeneBarplot Source code
moduleNumber Source code
modulecolor2 Source code
multiData.apply Source code
multiData.mapply Source code
multiData.rbindSelf Source code
multiData.simplify Source code
multiData.subset Source code
multiData2list Source code
multiLev2numeric Source code
multiSetMEs Source code
naiveAccuracyFnc Source code
nearestSNP Source code
networkPlot Source code
networkPlot.hierarchical Source code
normalizeAngle Source code
normalizeLabels Source code
orderMEMs Source code
orderMEs Source code
outlierMeasure Source code
outliers Source code
panel.cor Source code
panel.cor1 Source code
panel.hist Source code
peakRegions Source code
peaks2genes Source code
plotConnectivityGeneSignif1 Source code
plotEnrichmentBarplot Source code
plotEnrichments Source code
plotEnrichments.barplot Source code
plotHclustColors Source code
plotHistogramAndCF Source code
plotQTL Source code
pointToLabelDist Source code
predictvals Source code
prependZeros Source code
prettyNamesForMetaAnalysis Source code
print.flush Source code
printFlush Source code
processIndividualCluster Source code
propVarExplained Source code
qtlPeaks Source code
replaceNA Source code
reverseRows Source code
reverseVector Source code
rowConsensus Source code
runlengthSign Source code
scaleToRange Source code
scatterplot1 Source code
shiftSequence Source code
shortenLabels Source code
sigmoid1 Source code
signum1 Source code
simulateCausal Source code
smoothGauss Source code
spaste Source code
standardColors Source code
stderr1 Source code Source code
stretchLimits Source code
subsetMEMs Source code
table2.allLevels Source code
toDegrees Source code
toRadians Source code
topEnrichment Source code
validationSuccess Source code
validationSuccess.ext Source code
var1 Source code
varNames Source code
verboseMultiplot Source code
verbosePairs Source code
zeo Source code
mzinkgraf/ConsensusCoExpression documentation built on May 23, 2017, 9:32 a.m.