aligned	Generic.Roo
aligned,IdMapBase-method	aligned.IdMapBase
aligned.IdMapBase	aligned.IdMapBase
as.data.frame,IdMapBase-method	as.data.frame.IdMapBase
as.data.frame,JointIdMap-method	as.data.frame.JointIdMap
as.data.frame.IdMapBase	as.data.frame.IdMapBase
as.data.frame.JointIdMap	as.data.frame.JointIdMap
as.IdMap	Generic.Roo
as.IdMap,UniquePairs-method	as.IdMap.UniquePairs
as.IdMap.UniquePairs	as.IdMap.UniquePairs
as.list,IdMap-method	as.list.IdMap
as.list.IdMap	as.list.IdMap
as.MultiSet	Generic.Roo
as.MultiSet,CorrData-method	as.MultiSet.CorrData
as.MultiSet.CorrData	as.MultiSet.CorrData
as.UniquePairs	Generic.Roo
as.UniquePairs,IdMap-method	as.UniquePairs.IdMap
as.UniquePairs.IdMap	as.UniquePairs.IdMap
Bootstrap	Bootstrap
Bootstrap.plot	plot.Bootstrap
boxplot,JointUniquePairs-method	boxplot.JointUniquePairs
boxplot.JointUniquePairs	boxplot.JointUniquePairs
boxplotdataJitter	Generic.Roo
boxplotdataJitter,JointUniquePairs-method	boxplotdataJitter.JointUniquePairs
boxplotdataJitter.JointUniquePairs	boxplotdataJitter.JointUniquePairs
byColNames	Generic.Roo
byColNames,Subset-method	byColNames.Subset
byColNames.Subset	byColNames.Subset
byColumn	Generic.Roo
byColumn,Subset-method	byColumn.Subset
byColumn.Subset	byColumn.Subset
byRow	Generic.Roo
byRow,Subset-method	byRow.Subset
byRow.Subset	byRow.Subset
byRowNames	Generic.Roo
byRowNames,Subset-method	byRowNames.Subset
byRowNames.Subset	byRowNames.Subset
clust	Generic.Roo
clust,Mixture-method	clust.Mixture
clust.Mixture	clust.Mixture
copy	Generic.Roo
copy,Display-method	copy.Display
copy.Display	copy.Display
Corr	Corr
corr.boxplot	Generic.Roo
corr.boxplot,JointUniquePairs-method	corr.boxplot.JointUniquePairs
corr.boxplot.JointUniquePairs	corr.boxplot.JointUniquePairs
Corr.getData	getData.Corr
Corr.getUniquePairs	getUniquePairs.Corr
Corr.plot	plot.Corr
corr.plot	Generic.Roo
corr.plot,JointUniquePairs-method	corr.plot.JointUniquePairs
corr.plot.JointUniquePairs	corr.plot.JointUniquePairs
CorrData	CorrData
CorrData.as.MultiSet	as.MultiSet.CorrData
CorrData.getExperimentSet	getExperimentSet.CorrData
CorrData.getSampleNames	getSampleNames.CorrData
CorrData.getUniquePairs	getUniquePairs.CorrData
CorrData.interactive.plot	interactive.plot.CorrData
CorrData.pack.experiments	pack.experiments.CorrData
CorrData.plot	plot.CorrData
CorrData.primaryKey	primaryKey.CorrData
CorrData.secondaryKey	secondaryKey.CorrData
create	Generic.Roo
create,Display-method	create.Display
create,UniquePairs-method	create.UniquePairs
create.Display	create.Display
create.UniquePairs	create.UniquePairs
CsvList.merge	Generic.Roo
CsvList.merge,Misc-method	CsvList.merge.Misc
CsvList.merge.Misc	CsvList.merge.Misc
DataFilter	DataFilter
DataFilter.do.apply	do.apply.DataFilter
DataFilter.fisherTransform	fisherTransform.DataFilter
DataFilter.fisherTransformInverse	fisherTransformInverse.DataFilter
DataFilter.fisherTransformJacobean	fisherTransformJacobean.DataFilter
DataFilter.log10	log10.DataFilter
DataFilter.minAvgCountConstraint	minAvgCountConstraint.DataFilter
DataFilter.minCountConstraint	minCountConstraint.DataFilter
DataFilter.minCountGroupConstraint	minCountGroupConstraint.DataFilter
DataFilter.removeNASeries	removeNASeries.DataFilter
diffCounts.plot	Generic.Roo
diffCounts.plot,JointIdMap-method	diffCounts.plot.JointIdMap
diffCounts.plot.JointIdMap	diffCounts.plot.JointIdMap
dim,IdMapBase-method	dim.IdMapBase
dim.IdMapBase	dim.IdMapBase
dimnames,IdMapBase-method	dimnames.IdMapBase
dimnames.IdMapBase	dimnames.IdMapBase
Display	Display
Display.copy	copy.Display
Display.create	create.Display
Display.line.loess	line.loess.Display
Display.line.unsorted	line.unsorted.Display
Display.progressMsg	progressMsg.Display
Display.textBoundingBox	textBoundingBox.Display
Display.zoom.pars	zoom.pars.Display
do.apply	Generic.Roo
do.apply,DataFilter-method	do.apply.DataFilter
do.apply.DataFilter	do.apply.DataFilter
do.glm	Generic.Roo
do.glm,JointUniquePairs-method	do.glm.JointUniquePairs
do.glm.JointUniquePairs	do.glm.JointUniquePairs
ecdf.plot	Generic.Roo
ecdf.plot,JointIdMap-method	ecdf.plot.JointIdMap
ecdf.plot.JointIdMap	ecdf.plot.JointIdMap
equals,UniquePairs-method	equals.UniquePairs
equals.UniquePairs	equals.UniquePairs
examples	examples
fisherTransform	Generic.Roo
fisherTransform,DataFilter-method	fisherTransform.DataFilter
fisherTransform.DataFilter	fisherTransform.DataFilter
fisherTransformInverse	Generic.Roo
fisherTransformInverse,DataFilter-method	fisherTransformInverse.DataFilter
fisherTransformInverse.DataFilter	fisherTransformInverse.DataFilter
fisherTransformJacobean	Generic.Roo
fisherTransformJacobean,DataFilter-method	fisherTransformJacobean.DataFilter
fisherTransformJacobean.DataFilter	fisherTransformJacobean.DataFilter
Generic R.00 objects	Generic.Roo
getBootstrap	Generic.Roo
getBootstrap,JointUniquePairs-method	getBootstrap.JointUniquePairs
getBootstrap.JointUniquePairs	getBootstrap.JointUniquePairs
getCompoundEvents	Generic.Roo
getCompoundEvents,IdMapDiffCounts-method	getCompoundEvents.IdMapDiffCounts
getCompoundEvents.IdMapDiffCounts	getCompoundEvents.IdMapDiffCounts
getCompoundGroups	Generic.Roo
getCompoundGroups,IdMapDiffCounts-method	getCompoundGroups.IdMapDiffCounts
getCompoundGroups.IdMapDiffCounts	getCompoundGroups.IdMapDiffCounts
getCorr	Generic.Roo
getCorr,JointUniquePairs-method	getCorr.JointUniquePairs
getCorr.JointUniquePairs	getCorr.JointUniquePairs
getCorrData	Generic.Roo
getCorrData,JointUniquePairs-method	getCorrData.JointUniquePairs
getCorrData.JointUniquePairs	getCorrData.JointUniquePairs
getCorrDataFrame	Generic.Roo
getCorrDataFrame,JointUniquePairs-method	getCorrDataFrame.JointUniquePairs
getCorrDataFrame.JointUniquePairs	getCorrDataFrame.JointUniquePairs
getCounts	Generic.Roo
getCounts,IdMap-method	getCounts.IdMap
getCounts,JointIdMap-method	getCounts.JointIdMap
getCounts.IdMap	getCounts.IdMap
getCounts.JointIdMap	getCounts.JointIdMap
getData	Generic.Roo
getData,Corr-method	getData.Corr
getData,Mixture-method	getData.Mixture
getData.Corr	getData.Corr
getData.Mixture	getData.Mixture
getDiff	Generic.Roo
getDiff,JointIdMap-method	getDiff.JointIdMap
getDiff.JointIdMap	getDiff.JointIdMap
getExperimentSet	Generic.Roo
getExperimentSet,CorrData-method	getExperimentSet.CorrData
getExperimentSet.CorrData	getExperimentSet.CorrData
getIdMapList	Generic.Roo
getIdMapList,JointIdMap-method	getIdMapList.JointIdMap
getIdMapList.JointIdMap	getIdMapList.JointIdMap
getMapNames	Generic.Roo
getMapNames,JointIdMap-method	getMapNames.JointIdMap
getMapNames,JointUniquePairs-method	getMapNames.JointUniquePairs
getMapNames.JointIdMap	getMapNames.JointIdMap
getMapNames.JointUniquePairs	getMapNames.JointUniquePairs
getMatch	Generic.Roo
getMatch,UniquePairs-method	getMatch.UniquePairs
getMatch.UniquePairs	getMatch.UniquePairs
getMatchInfo	Generic.Roo
getMatchInfo,JointIdMap-method	getMatchInfo.JointIdMap
getMatchInfo,JointUniquePairs-method	getMatchInfo.JointUniquePairs
getMatchInfo.JointIdMap	getMatchInfo.JointIdMap
getMatchInfo.JointUniquePairs	getMatchInfo.JointUniquePairs
getMixture	Generic.Roo
getMixture,JointUniquePairs-method	getMixture.JointUniquePairs
getMixture.JointUniquePairs	getMixture.JointUniquePairs
getName,IdMapBase-method	getName.IdMapBase
getName.IdMapBase	getName.IdMapBase
getSampleNames	Generic.Roo
getSampleNames,CorrData-method	getSampleNames.CorrData
getSampleNames.CorrData	getSampleNames.CorrData
getStats	Generic.Roo
getStats,IdMapCounts-method	getStats.IdMapCounts
getStats,Mixture-method	getStats.Mixture
getStats.IdMapCounts	getStats.IdMapCounts
getStats.Mixture	getStats.Mixture
getUnionIdMap	Generic.Roo
getUnionIdMap,JointIdMap-method	getUnionIdMap.JointIdMap
getUnionIdMap.JointIdMap	getUnionIdMap.JointIdMap
getUniquePairs	Generic.Roo
getUniquePairs,Corr-method	getUniquePairs.Corr
getUniquePairs,CorrData-method	getUniquePairs.CorrData
getUniquePairs,JointUniquePairs-method	getUniquePairs.JointUniquePairs
getUniquePairs.Corr	getUniquePairs.Corr
getUniquePairs.CorrData	getUniquePairs.CorrData
getUniquePairs.JointUniquePairs	getUniquePairs.JointUniquePairs
IdMap	IdMap
IdMap.as.list	as.list.IdMap
IdMap.as.UniquePairs	as.UniquePairs.IdMap
IdMap.getCounts	getCounts.IdMap
IdMap.merge	merge.IdMap
IdMap.swapKeys	swapKeys.IdMap
IdMapBase	IdMapBase
IdMapBase.aligned	aligned.IdMapBase
IdMapBase.as.data.frame	as.data.frame.IdMapBase
IdMapBase.dim	dim.IdMapBase
IdMapBase.dimnames	dimnames.IdMapBase
IdMapBase.getName	getName.IdMapBase
IdMapBase.primaryIDs	primaryIDs.IdMapBase
IdMapBase.primaryKey	primaryKey.IdMapBase
IdMapBase.secondaryKey	secondaryKey.IdMapBase
IdMapBase.[	000-LB-.IdMapBase
IdMapCounts	IdMapCounts
IdMapCounts.getStats	getStats.IdMapCounts
IdMapCounts.plot	plot.IdMapCounts
IdMapDiff	IdMapDiff
IdMapDiffCounts	IdMapDiffCounts
IdMapDiffCounts.getCompoundEvents	getCompoundEvents.IdMapDiffCounts
IdMapDiffCounts.getCompoundGroups	getCompoundGroups.IdMapDiffCounts
IdMapDiffCounts.plot	plot.IdMapDiffCounts
IdMapDiffCounts.summary	summary.IdMapDiffCounts
IdMappingAnalysis	IdMappingAnalysis-dash-package
interactive.corr.boxplot	Generic.Roo
interactive.corr.boxplot,JointUniquePairs-method	interactive.corr.boxplot.JointUniquePairs
interactive.corr.boxplot.JointUniquePairs	interactive.corr.boxplot.JointUniquePairs
interactive.corr.plot	Generic.Roo
interactive.corr.plot,JointUniquePairs-method	interactive.corr.plot.JointUniquePairs
interactive.corr.plot.JointUniquePairs	interactive.corr.plot.JointUniquePairs
interactive.mixture.boxplot	Generic.Roo
interactive.mixture.boxplot,JointUniquePairs-method	interactive.mixture.boxplot.JointUniquePairs
interactive.mixture.boxplot.JointUniquePairs	interactive.mixture.boxplot.JointUniquePairs
interactive.mixture.plot	Generic.Roo
interactive.mixture.plot,JointUniquePairs-method	interactive.mixture.plot.JointUniquePairs
interactive.mixture.plot.JointUniquePairs	interactive.mixture.plot.JointUniquePairs
interactive.plot	Generic.Roo
interactive.plot,CorrData-method	interactive.plot.CorrData
interactive.plot,JointUniquePairs-method	interactive.plot.JointUniquePairs
interactive.plot.CorrData	interactive.plot.CorrData
interactive.plot.JointUniquePairs	interactive.plot.JointUniquePairs
interleave	Generic.Roo
interleave,Misc-method	interleave.Misc
interleave.Misc	interleave.Misc
JointIdMap	JointIdMap
JointIdMap.as.data.frame	as.data.frame.JointIdMap
JointIdMap.diffCounts.plot	diffCounts.plot.JointIdMap
JointIdMap.ecdf.plot	ecdf.plot.JointIdMap
JointIdMap.getCounts	getCounts.JointIdMap
JointIdMap.getDiff	getDiff.JointIdMap
JointIdMap.getIdMapList	getIdMapList.JointIdMap
JointIdMap.getMapNames	getMapNames.JointIdMap
JointIdMap.getMatchInfo	getMatchInfo.JointIdMap
JointIdMap.getUnionIdMap	getUnionIdMap.JointIdMap
JointUniquePairs	JointUniquePairs
JointUniquePairs.boxplot	boxplot.JointUniquePairs
JointUniquePairs.boxplotdataJitter	boxplotdataJitter.JointUniquePairs
JointUniquePairs.corr.boxplot	corr.boxplot.JointUniquePairs
JointUniquePairs.corr.plot	corr.plot.JointUniquePairs
JointUniquePairs.do.glm	do.glm.JointUniquePairs
JointUniquePairs.getBootstrap	getBootstrap.JointUniquePairs
JointUniquePairs.getCorr	getCorr.JointUniquePairs
JointUniquePairs.getCorrData	getCorrData.JointUniquePairs
JointUniquePairs.getCorrDataFrame	getCorrDataFrame.JointUniquePairs
JointUniquePairs.getMapNames	getMapNames.JointUniquePairs
JointUniquePairs.getMatchInfo	getMatchInfo.JointUniquePairs
JointUniquePairs.getMixture	getMixture.JointUniquePairs
JointUniquePairs.getUniquePairs	getUniquePairs.JointUniquePairs
JointUniquePairs.interactive.corr.boxplot	interactive.corr.boxplot.JointUniquePairs
JointUniquePairs.interactive.corr.plot	interactive.corr.plot.JointUniquePairs
JointUniquePairs.interactive.mixture.boxplot	interactive.mixture.boxplot.JointUniquePairs
JointUniquePairs.interactive.mixture.plot	interactive.mixture.plot.JointUniquePairs
JointUniquePairs.interactive.plot	interactive.plot.JointUniquePairs
JointUniquePairs.mixture.boxplot	mixture.boxplot.JointUniquePairs
JointUniquePairs.mixture.plot	mixture.plot.JointUniquePairs
JointUniquePairs.subsetCorr	subsetCorr.JointUniquePairs
JointUniquePairs.subsetData	subsetData.JointUniquePairs
JointUniquePairs.subsetGroups	subsetGroups.JointUniquePairs
line.loess	Generic.Roo
line.loess,Display-method	line.loess.Display
line.loess.Display	line.loess.Display
line.unsorted	Generic.Roo
line.unsorted,Display-method	line.unsorted.Display
line.unsorted.Display	line.unsorted.Display
log10,DataFilter-method	log10.DataFilter
log10.DataFilter	log10.DataFilter
merge,IdMap-method	merge.IdMap
merge.IdMap	merge.IdMap
minAvgCountConstraint	Generic.Roo
minAvgCountConstraint,DataFilter-method	minAvgCountConstraint.DataFilter
minAvgCountConstraint.DataFilter	minAvgCountConstraint.DataFilter
minCountConstraint	Generic.Roo
minCountConstraint,DataFilter-method	minCountConstraint.DataFilter
minCountConstraint.DataFilter	minCountConstraint.DataFilter
minCountGroupConstraint	Generic.Roo
minCountGroupConstraint,DataFilter-method	minCountGroupConstraint.DataFilter
minCountGroupConstraint.DataFilter	minCountGroupConstraint.DataFilter
Misc	Misc
Misc.CsvList.merge	CsvList.merge.Misc
Misc.interleave	interleave.Misc
Misc.to.base	to.base.Misc
Misc.to.binary.logical	to.binary.logical.Misc
Misc.to.index.expr	to.index.expr.Misc
Misc.words	words.Misc
Mixture	Mixture
mixture.boxplot	Generic.Roo
mixture.boxplot,JointUniquePairs-method	mixture.boxplot.JointUniquePairs
mixture.boxplot.JointUniquePairs	mixture.boxplot.JointUniquePairs
Mixture.clust	clust.Mixture
Mixture.getData	getData.Mixture
Mixture.getStats	getStats.Mixture
Mixture.plot	plot.Mixture
mixture.plot	Generic.Roo
mixture.plot,JointUniquePairs-method	mixture.plot.JointUniquePairs
mixture.plot.JointUniquePairs	mixture.plot.JointUniquePairs
Mixture.primaryKey	primaryKey.Mixture
Mixture.secondaryKey	secondaryKey.Mixture
pack.experiments	Generic.Roo
pack.experiments,CorrData-method	pack.experiments.CorrData
pack.experiments.CorrData	pack.experiments.CorrData
plot,Bootstrap-method	plot.Bootstrap
plot,Corr-method	plot.Corr
plot,CorrData-method	plot.CorrData
plot,IdMapCounts-method	plot.IdMapCounts
plot,IdMapDiffCounts-method	plot.IdMapDiffCounts
plot,Mixture-method	plot.Mixture
plot.Bootstrap	plot.Bootstrap
plot.Corr	plot.Corr
plot.CorrData	plot.CorrData
plot.IdMapCounts	plot.IdMapCounts
plot.IdMapDiffCounts	plot.IdMapDiffCounts
plot.Mixture	plot.Mixture
primaryIDs	Generic.Roo
primaryIDs,IdMapBase-method	primaryIDs.IdMapBase
primaryIDs.IdMapBase	primaryIDs.IdMapBase
primaryKey	Generic.Roo
primaryKey,CorrData-method	primaryKey.CorrData
primaryKey,IdMapBase-method	primaryKey.IdMapBase
primaryKey,Mixture-method	primaryKey.Mixture
primaryKey.CorrData	primaryKey.CorrData
primaryKey.IdMapBase	primaryKey.IdMapBase
primaryKey.Mixture	primaryKey.Mixture
progressMsg	Generic.Roo
progressMsg,Display-method	progressMsg.Display
progressMsg.Display	progressMsg.Display
removeNASeries	Generic.Roo
removeNASeries,DataFilter-method	removeNASeries.DataFilter
removeNASeries.DataFilter	removeNASeries.DataFilter
secondaryKey	Generic.Roo
secondaryKey,CorrData-method	secondaryKey.CorrData
secondaryKey,IdMapBase-method	secondaryKey.IdMapBase
secondaryKey,Mixture-method	secondaryKey.Mixture
secondaryKey.CorrData	secondaryKey.CorrData
secondaryKey.IdMapBase	secondaryKey.IdMapBase
secondaryKey.Mixture	secondaryKey.Mixture
Subset	Subset
Subset.byColNames	byColNames.Subset
Subset.byColumn	byColumn.Subset
Subset.byRow	byRow.Subset
Subset.byRowNames	byRowNames.Subset
subsetCorr	Generic.Roo
subsetCorr,JointUniquePairs-method	subsetCorr.JointUniquePairs
subsetCorr.JointUniquePairs	subsetCorr.JointUniquePairs
subsetData	Generic.Roo
subsetData,JointUniquePairs-method	subsetData.JointUniquePairs
subsetData.JointUniquePairs	subsetData.JointUniquePairs
subsetGroups	Generic.Roo
subsetGroups,JointUniquePairs-method	subsetGroups.JointUniquePairs
subsetGroups.JointUniquePairs	subsetGroups.JointUniquePairs
summary,IdMapDiffCounts-method	summary.IdMapDiffCounts
summary.IdMapDiffCounts	summary.IdMapDiffCounts
swapKeys	Generic.Roo
swapKeys,IdMap-method	swapKeys.IdMap
swapKeys,UniquePairs-method	swapKeys.UniquePairs
swapKeys.IdMap	swapKeys.IdMap
swapKeys.UniquePairs	swapKeys.UniquePairs
textBoundingBox	Generic.Roo
textBoundingBox,Display-method	textBoundingBox.Display
textBoundingBox.Display	textBoundingBox.Display
to.base	Generic.Roo
to.base,Misc-method	to.base.Misc
to.base.Misc	to.base.Misc
to.binary.logical	Generic.Roo
to.binary.logical,Misc-method	to.binary.logical.Misc
to.binary.logical.Misc	to.binary.logical.Misc
to.index.expr	Generic.Roo
to.index.expr,Misc-method	to.index.expr.Misc
to.index.expr.Misc	to.index.expr.Misc
unique,UniquePairs-method	unique.UniquePairs
unique.UniquePairs	unique.UniquePairs
UniquePairs	UniquePairs
UniquePairs.as.IdMap	as.IdMap.UniquePairs
UniquePairs.create	create.UniquePairs
UniquePairs.equals	equals.UniquePairs
UniquePairs.getMatch	getMatch.UniquePairs
UniquePairs.swapKeys	swapKeys.UniquePairs
UniquePairs.unique	unique.UniquePairs
words	Generic.Roo
words,Misc-method	words.Misc
words.Misc	words.Misc
zoom.pars	Generic.Roo
zoom.pars,Display-method	zoom.pars.Display
zoom.pars.Display	zoom.pars.Display
[,IdMapBase-method	000-LB-.IdMapBase
[.IdMapBase	000-LB-.IdMapBase
