API for dbottomly/HitWalker
Network-based variant prioriziation using functional assay scores

Global functions
HitWalker Man page
HitWalker-package Man page
add.in.missing.nodes Man page Source code
additionalIDs Man page
additionalIDs,priorDbParams-method Man page
additionalIDs<- Man page
additionalIDs<-,priorDbParams-method Man page
annotQuery Man page
annotQuery,priorDbParams-method Man page
annotQuery<- Man page
annotQuery<-,priorDbParams-method Man page
annotatedIGraph Man page
annotatedIGraph-class Man page
annotation Man page
annotation,annotatedIGraph-method Man page
annotation<- Man page
annotation<-,annotatedIGraph-method Man page
base.query.func Source code
base.score.summary.func Source code
basePriorDbParams Source code
baseTestQuery Source code
basic.plot.image Source code
basicLabelFuncList Source code
check.col.data.frame Source code
check.db.params Source code
check.label.params Source code
check.sample.id.list Source code
collapse.nodes.genes Man page Source code
collapseChar Man page
collapseChar,graphDispParams-method Man page
collapseChar<- Man page
collapseChar<-,graphDispParams-method Man page
combScoreName Man page
combScoreName,priorDbParams-method Man page
combScoreName<- Man page
combScoreName<-,priorDbParams-method Man page
coreID Man page
coreID,priorDbParams-method Man page
coreID<- Man page
coreID<-,priorDbParams-method Man page
default.fail Source code
default.score.summary.func Source code
defaultAnnotQuery Source code
defaultBorder Man page
defaultBorder,graphDispParams-method Man page
defaultBorder<- Man page
defaultBorder<-,graphDispParams-method Man page
defaultColor Man page
defaultColor,graphDispParams-method Man page
defaultColor<- Man page
defaultColor<-,graphDispParams-method Man page
defaultFuncSummaryMap Source code
defaultGraphTransFunc Source code
defaultHitQuery Source code
defaultLLSAnnotQuery Source code
defaultLLSHitQuery Source code
defaultLLSMatrixQuery Source code
defaultLLSPriorDbParams Source code
defaultLLSVariantQuery Source code
defaultLabelFuncList Source code
defaultMatrixQuery Source code
defaultNodeCombFunc Source code
defaultPatientOverlay Source code
defaultPriorDbParams Source code
defaultRwrParams Source code Source code
defaultShapeMappingFunc Source code
defaultStyleMappingFunc Source code
defaultVariantFilter Source code
defaultVariantQuery Source code
draw.graph Man page Source code
draw.graph.variantPriorResult Man page Source code
draw.multiline.text Source code
draw.rectangle Source code
draw.triangle Source code
drawAgNodeTG Source code
ellipse Source code
fileName Man page
fileName,graphDispParams-method Man page
fileName<- Man page
fileName<-,graphDispParams-method Man page
filter.variant.annots Man page Source code
filterBestCategory Man page
filterBestCategory,variantFilter-method Man page
filterCategory Man page
filterCategory,variantFilter-method Man page
filterCollapseCol Man page
filterCollapseCol,variantFilter-method Man page
filterDta Man page
filterDta,variantFilter-method Man page
filterIgnoreCol Man page
filterIgnoreCol,variantFilter-method Man page
filterLabels Man page
filterLabels,variantFilter-method Man page
filterSep Man page
filterSep,variantFilter-method Man page
freq.label Source code
get.graph.sp Man page Source code
get.hit.prots Man page Source code
get.protein.protein.graph Man page Source code
get.sample.overlays Man page Source code
get.sample.variants Man page Source code
getBestVarText Man page
getBestVarText,variantPriorResult-method Man page
getBordColors Man page
getBordColors,variantPriorResult-method Man page
getConvergeMaxIt Man page
getConvergeMaxIt,rwrParams-method Man page
getConvergeThresh Man page
getConvergeThresh,rwrParams-method Man page
getFillColors Man page
getFillColors,variantPriorResult-method Man page
getFilterBestCategory Man page
getFilterBestCategory,priorDbParams-method Man page
getFilterCategory Man page
getFilterCategory,priorDbParams-method Man page
getFilterCollapseCol Man page
getFilterCollapseCol,priorDbParams-method Man page
getFilterIgnoreCol Man page
getFilterIgnoreCol,priorDbParams-method Man page
getFilterLabels Man page
getFilterLabels,priorDbParams-method Man page
getFilterSep Man page
getFilterSep,priorDbParams-method Man page
getFilterValues Man page
getFilterValues,priorDbParams-method Man page
getGraph Man page
getGraph,annotatedIGraph-method Man page
getGraph,variantPriorResult-method Man page
getHitDta Man page
getHitDta,variantPriorResult-method Man page
getHitSummaryID Man page
getHitSummaryID,variantPriorResult-method Man page
getNodeShapes Man page
getNodeShapes,variantPriorResult-method Man page
getNodeStyles Man page
getNodeStyles,variantPriorResult-method Man page
getParameters Man page
getParameters,variantPriorResult-method Man page
getProteinScores Man page
getProteinScores,variantPriorResult-method Man page
getProxDta Man page
getProxDta,variantPriorResult-method Man page
getProxRankCol Man page
getProxRankCol,variantPriorResult-method Man page
getProxSummaryID Man page
getProxSummaryID,variantPriorResult-method Man page
getProxTypeCol Man page
getProxTypeCol,variantPriorResult-method Man page
getRankedQueries Man page
getRankedQueries,variantPriorResult-method Man page
getRestartProb Man page
getRestartProb,rwrParams-method Man page
getSampleName Man page
getSampleName,variantPriorResult-method Man page
getSummarizationLevel Man page
getSummarizationLevel,priorDbParams-method Man page
getVarDta Man page
getVarDta,variantPriorResult-method Man page
getVarSummaryID Man page
getVarSummaryID,variantPriorResult-method Man page
graphDispParams Man page
graphDispParams-class Man page
height Man page
height,graphDispParams-method Man page
height<- Man page
height<-,graphDispParams-method Man page
hitColors Man page
hitColors,graphDispParams-method Man page
hitColors<- Man page
hitColors<-,graphDispParams-method Man page
hitQuery Man page
hitQuery,priorDbParams-method Man page
hitQuery<- Man page
hitQuery<-,priorDbParams-method Man page
idTable Man page
idTable,priorDbParams-method Man page
idTable<- Man page
idTable<-,priorDbParams-method Man page
igraph.to.graphNEL.slim Source code
kBestShortestPathsIgraph Source code
labelFuncList Man page
labelFuncList,graphDispParams-method Man page
labelFuncList<- Man page
labelFuncList<-,graphDispParams-method Man page
labelSep Man page
labelSep,graphDispParams-method Man page
labelSep<- Man page
labelSep<-,graphDispParams-method Man page
lls.plot.image Source code
loadGraph Man page Source code
make.target.graph Man page Source code
make.target.graph.kbest Source code
makeGraphDispParams Man page Source code
makeRwrParams Man page Source code
makeVariantFilter Man page Source code
makeVariantPriorResult Man page Source code
matrixQuery Man page
matrixQuery,priorDbParams-method Man page
matrixQuery<- Man page
matrixQuery<-,priorDbParams-method Man page
maxPlotHits Man page
maxPlotHits,graphDispParams-method Man page
maxPlotHits<- Man page
maxPlotHits<-,graphDispParams-method Man page
maxPlotVars Man page
maxPlotVars,graphDispParams-method Man page
maxPlotVars<- Man page
maxPlotVars<-,graphDispParams-method Man page
multi.shading Source code
nameTextSep Man page
nameTextSep,graphDispParams-method Man page
nameTextSep<- Man page
nameTextSep<-,graphDispParams-method Man page
no.label Source code
nodeCombinationFunc Man page
nodeCombinationFunc,graphDispParams-method Man page
nodeCombinationFunc<- Man page
nodeCombinationFunc<-,graphDispParams-method Man page
nodeWeightCol Man page
nodeWeightCol,priorDbParams-method Man page
patVarID Man page
patVarID,priorDbParams-method Man page
patVarID<- Man page
patVarID<-,priorDbParams-method Man page
patientFilterCol Man page
patientFilterCol,priorDbParams-method Man page
patientFilterCol<- Man page
patientFilterCol<-,priorDbParams-method Man page
patientFreqCol Man page
patientFreqCol,priorDbParams-method Man page
patientFreqCol<- Man page
patientFreqCol<-,priorDbParams-method Man page
patientOverlay Man page
patientOverlay,priorDbParams-method Man page
patientOverlay<- Man page
patientOverlay<-,priorDbParams-method Man page
plot Man page
plot.target.graph Source code
plotFunc Man page
plotFunc,graphDispParams-method Man page
plotFunc<- Man page
plotFunc<-,graphDispParams-method Man page
possibleIdCols Man page
possibleIdCols,priorDbParams-method Man page
possibleIdCols<- Man page
possibleIdCols<-,priorDbParams-method Man page
prior.obj Man page
priorDbParams Man page
priorDbParams-class Man page
process.node.annot Man page Source code
protein.list.to.gene Man page Source code
qa.qc.label Source code
queryColor Man page
queryColor,graphDispParams-method Man page
queryColor<- Man page
queryColor<-,graphDispParams-method Man page
queryLabel Man page
queryLabel,priorDbParams-method Man page
queryLabel<- Man page
queryLabel<-,priorDbParams-method Man page
queryParams Man page
queryParams,priorDbParams-method Man page
queryParams<- Man page
queryParams<-,priorDbParams-method Man page
random.walk Man page Source code
rank.label Source code
reconcile.sample.name Man page Source code
reconciledIdCol Man page
reconciledIdCol,priorDbParams-method Man page
reconciledIdCol<- Man page
reconciledIdCol<-,priorDbParams-method Man page
remove.annot.dup Source code
retrieve.param.query Man page Source code
run.prioritization.patient Man page Source code
run.protocol Man page Source code
rwrParams Man page
rwrParams-class Man page
rwrParamsObj Man page
rwrParamsObj,priorDbParams-method Man page
rwrParamsObj<- Man page
rwrParamsObj<-,priorDbParams-method Man page
sampleIdCol Man page
sampleIdCol,priorDbParams-method Man page
sampleIdCol<- Man page
sampleIdCol<-,priorDbParams-method Man page
saveGraph Man page
saveGraph,annotatedIGraph-method Man page
scoreSummaryFunc Man page
scoreSummaryFunc,priorDbParams-method Man page
scoreSummaryFunc<- Man page
scoreSummaryFunc<-,priorDbParams-method Man page
seedLabel Man page
seedLabel,priorDbParams-method Man page
seedLabel<- Man page
seedLabel<-,priorDbParams-method Man page
shapeFunc Man page
shapeFunc,graphDispParams-method Man page
shapeFunc<- Man page
shapeFunc<-,graphDispParams-method Man page
show,annotatedIGraph-method Man page
show,graphDispParams-method Man page
show,priorDbParams-method Man page
show,rwrParams-method Man page
show,variantFilter-method Man page
show,variantPriorResult-method Man page
styleFunc Man page
styleFunc,graphDispParams-method Man page
styleFunc<- Man page
styleFunc<-,graphDispParams-method Man page
summary,variantPriorResult-method Man page
summaryID Man page
summaryID,priorDbParams-method Man page
summaryID<- Man page
summaryID<-,priorDbParams-method Man page
summaryMap Man page
summaryMap,priorDbParams-method Man page
summaryMap<- Man page
summaryMap<-,priorDbParams-method Man page
testHitQuery Source code
testPatientOverlay Source code
testPriorDbParams Source code
testVariantQuery Source code
transformGraph Man page
transformGraph,priorDbParams-method Man page
transformGraph<- Man page
transformGraph<-,priorDbParams-method Man page
variantFilter Man page
variantFilter-class Man page
variantFilterObj Man page
variantFilterObj,priorDbParams-method Man page
variantFilterObj<- Man page
variantFilterObj<-,priorDbParams-method Man page
variantPriorResult Man page
variantPriorResult-class Man page
variantQuery Man page
variantQuery,priorDbParams-method Man page
variantQuery<- Man page
variantQuery<-,priorDbParams-method Man page
variantTypeCol Man page
variantTypeCol,priorDbParams-method Man page
variantTypeCol<- Man page
variantTypeCol<-,priorDbParams-method Man page
verbLevel Man page
verbLevel,priorDbParams-method Man page
verbLevel,rwrParams-method Man page
verbLevel<- Man page
verbLevel<-,priorDbParams-method Man page
width Man page
width,graphDispParams-method Man page
width<- Man page
width<-,graphDispParams-method Man page
dbottomly/HitWalker documentation built on May 12, 2017, 9:05 p.m.