abcdDNA	abcdDNA
absoluteCN	absoluteCN
absoluteCN,data.frame,matrix,GCAdjustParams-method	absoluteCN
absoluteCN,GRanges,matrix,GCAdjustParams-method	absoluteCN
AdjustedCopyEstimate	AdjustedCopyEstimate-class
AdjustedCopyEstimate,numeric,GRanges,numeric,numeric,matrix,list,matrix,character-method	AdjustedCopyEstimate-class
AdjustedCopyEstimate-class	AdjustedCopyEstimate-class
AffymetrixCdfFile	AffymetrixCdfFile-class
AffymetrixCdfFile-class	AffymetrixCdfFile-class
AffymetrixCelSet	AffymetrixCelSet-class
AffymetrixCelSet-class	AffymetrixCelSet-class
annoDF2GR	annoDF2GR
annoDF2GR,data.frame-method	annoDF2GR
annoGR2DF	annoGR2DF
annoGR2DF,GRanges-method	annoGR2DF
annotationBlocksCounts	annotationBlocksCounts
annotationBlocksCounts,ANY,data.frame-method	annotationBlocksCounts
annotationBlocksCounts,character,GRanges-method	annotationBlocksCounts
annotationBlocksCounts,GRanges,GRanges-method	annotationBlocksCounts
annotationBlocksCounts,GRangesList,GRanges-method	annotationBlocksCounts
annotationBlocksLookup	annotationBlocksLookup
annotationBlocksLookup,data.frame,data.frame-method	annotationBlocksLookup
annotationBlocksLookup,data.frame,GRanges-method	annotationBlocksLookup
annotationCounts	annotationCounts
annotationCounts,ANY,data.frame-method	annotationCounts
annotationCounts,ANY,GRanges-method	annotationCounts
annotationLookup	annotationLookup
annotationLookup,data.frame,data.frame-method	annotationLookup
annotationLookup,data.frame,GRanges-method	annotationLookup
BAM2GRanges	BAM2GRanges
BAM2GRanges,character-method	BAM2GRanges
BAM2GRangesList	BAM2GRanges
BAM2GRangesList,character-method	BAM2GRanges
Basic_Statistics	FastQC-class
Basic_Statistics,FastQC-method	FastQC-class
Basic_Statistics,SequenceQC-method	FastQC-class
Basic_Statistics,SequenceQCSet-method	FastQC-class
BayMethList	BayMethList-class
BayMethList,GRanges,matrix,matrix,numeric-method	BayMethList-class
BayMethList-class	BayMethList-class
binPlots	binPlots
binPlots,ScoresList-method	binPlots
blocks	ChromaResults-class
blocks,ChromaResults-method	ChromaResults-class
blocksStats	blocksStats
blocksStats,ANY,data.frame-method	blocksStats
blocksStats,ANY,GRanges-method	blocksStats
checkProbes	checkProbes
checkProbes,data.frame,data.frame-method	checkProbes
checkProbes,GRanges,GRanges-method	checkProbes
chr21genes	chr21genes
ChromaBlocks	ChromaBlocks
ChromaBlocks,GRangesList,GRangesList-method	ChromaBlocks
ChromaResults	ChromaResults-class
ChromaResults-class	ChromaResults-class
chromosomeCNplots	chromosomeCNplots
chromosomeCNplots,AdjustedCopyEstimate-method	chromosomeCNplots
chromosomeCNplots,CopyEstimate-method	chromosomeCNplots
class:ChromaResults	ChromaResults-class
class:FastQC	FastQC-class
class:QdnaData	QdnaData
class:RegionStats	regionStats
class:SequenceQC	FastQC-class
class:SequenceQCSet	FastQC-class
ClusteredScoresList	ClusteredScoresList-class
ClusteredScoresList,ScoresList-method	ClusteredScoresList-class
ClusteredScoresList-class	ClusteredScoresList-class
clusterPlots	clusterPlots
clusterPlots,ClusteredScoresList-method	clusterPlots
clusterPlots,ScoresList-method	clusterPlots
clusters	ClusteredScoresList-class
clusters,ClusteredScoresList-method	ClusteredScoresList-class
control	BayMethList-class
control,BayMethList-method	BayMethList-class
control<-	BayMethList-class
control<-,BayMethList-method	BayMethList-class
CopyEstimate	CopyEstimate-class
CopyEstimate,GRanges,matrix,GRangesList,character-method	CopyEstimate-class
CopyEstimate-class	CopyEstimate-class
cpgBoxplots	cpgBoxPlots
cpgBoxplots,AffymetrixCelSet-method	cpgBoxPlots
cpgBoxplots,matrix-method	cpgBoxPlots
cpgDens	BayMethList-class
cpgDens,BayMethList-method	BayMethList-class
cpgDens<-	BayMethList-class
cpgDens<-,BayMethList-method	BayMethList-class
cpgDensityCalc	cpgDensityCalc
cpgDensityCalc,data.frame,BSgenome-method	cpgDensityCalc
cpgDensityCalc,GRanges,BSgenome-method	cpgDensityCalc
cpgDensityCalc,GRangesList,BSgenome-method	cpgDensityCalc
cpgDensityPlot	cpgDensityPlot
cpgDensityPlot,GRangesList-method	cpgDensityPlot
cutoff	ChromaResults-class
cutoff,ChromaResults-method	ChromaResults-class
determineOffset	determineOffset
empBayes	empBayes
enrichmentCalc	enrichmentCalc
enrichmentCalc,GRanges-method	enrichmentCalc
enrichmentCalc,GRangesList-method	enrichmentCalc
enrichmentPlot	enrichmentPlot
enrichmentPlot,GRangesList-method	enrichmentPlot
expr	expr
FastQC-class	FastQC-class
FDRTable	ChromaResults-class
FDRTable,ChromaResults-method	ChromaResults-class
featureBlocks	featureBlocks
featureBlocks,data.frame-method	featureBlocks
featureBlocks,GRanges-method	featureBlocks
featureScores	featureScores
featureScores,ANY,data.frame-method	featureScores
featureScores,ANY,GRanges-method	featureScores
findClusters	findClusters
fOffset	BayMethList-class
fOffset,BayMethList-method	BayMethList-class
fOffset<-	BayMethList-class
fOffset<-,BayMethList-method	BayMethList-class
GCadjustCopy	GCadjustCopy
GCadjustCopy,data.frame,matrix,GCAdjustParams-method	GCadjustCopy
GCadjustCopy,GRanges,matrix,GCAdjustParams-method	GCadjustCopy
GCAdjustParams	GCAdjustParams-class
GCAdjustParams,BSgenome,MappabilitySource-method	GCAdjustParams-class
GCAdjustParams-class	GCAdjustParams-class
GCbiasPlots	GCbiasPlots
GCbiasPlots,AdjustedCopyEstimate-method	GCbiasPlots
gcContentCalc	gcContentCalc
gcContentCalc,data.frame,BSgenome-method	gcContentCalc
gcContentCalc,GRanges,BSgenome-method	gcContentCalc
genomeBlocks	genomeBlocks
genomeBlocks,BSgenome-method	genomeBlocks
genomeBlocks,numeric-method	genomeBlocks
genQC	genQC
genQC,character-method	genQC
genQC,SequenceQCSet-method	genQC
getProbePositionsDf	getProbePositionsDf
getProbePositionsDf,AffymetrixCdfFile-method	getProbePositionsDf
getSampleOffsets	getSampleOffsets
hcRegions	hcRegions
hyperg2F1_vec	hyper
length	BayMethList-class
length,BayMethList-method	BayMethList-class
length,ScoresList-method	ScoresList-class
loadPairFile	loadPairFile
loadSampleDirectory	loadSampleDirectory
makeWindowLookupTable	makeWindowLookupTable
mappabilityCalc	mappabilityCalc
mappabilityCalc,data.frame,MappabilitySource-method	mappabilityCalc
mappabilityCalc,GRanges,MappabilitySource-method	mappabilityCalc
MappabilitySource	MappabilitySource-class
MappabilitySource-class	MappabilitySource-class
maskEmpBayes	BayMethList-class
maskEmpBayes,BayMethList-method	BayMethList-class
maskEmpBayes<-	BayMethList-class
maskEmpBayes<-,BayMethList-method	BayMethList-class
maskOut	maskOut
mergeReplicates	mergeReplicates
mergeReplicates,GRangesList-method	mergeReplicates
methEst	BayMethList-class
methEst,BayMethList-method	BayMethList-class
methEst<-	BayMethList-class
methEst<-,BayMethList-method	BayMethList-class
methylEst	methylEst
Mismatches	FastQC-class
Mismatches,SequenceQC-method	FastQC-class
Mismatches,SequenceQCSet-method	FastQC-class
MismatchTable	FastQC-class
MismatchTable,SequenceQC-method	FastQC-class
MismatchTable,SequenceQCSet-method	FastQC-class
multiHeatmap	multiHeatmap
names,ScoresList-method	ScoresList-class
names<-,ScoresList-method	ScoresList-class
ncontrol	BayMethList-class
ncontrol,BayMethList-method	BayMethList-class
nsampleInterest	BayMethList-class
nsampleInterest,BayMethList-method	BayMethList-class
Overrepresented_sequences	FastQC-class
Overrepresented_sequences,FastQC-method	FastQC-class
Overrepresented_sequences,SequenceQC-method	FastQC-class
Overrepresented_sequences,SequenceQCSet-method	FastQC-class
Per_base_GC_content	FastQC-class
Per_base_GC_content,FastQC-method	FastQC-class
Per_base_GC_content,SequenceQC-method	FastQC-class
Per_base_GC_content,SequenceQCSet-method	FastQC-class
Per_base_N_content	FastQC-class
Per_base_N_content,FastQC-method	FastQC-class
Per_base_N_content,SequenceQC-method	FastQC-class
Per_base_N_content,SequenceQCSet-method	FastQC-class
Per_base_sequence_content	FastQC-class
Per_base_sequence_content,FastQC-method	FastQC-class
Per_base_sequence_content,SequenceQC-method	FastQC-class
Per_base_sequence_content,SequenceQCSet-method	FastQC-class
Per_base_sequence_quality	FastQC-class
Per_base_sequence_quality,FastQC-method	FastQC-class
Per_base_sequence_quality,SequenceQC-method	FastQC-class
Per_base_sequence_quality,SequenceQCSet-method	FastQC-class
Per_sequence_GC_content	FastQC-class
Per_sequence_GC_content,FastQC-method	FastQC-class
Per_sequence_GC_content,SequenceQC-method	FastQC-class
Per_sequence_GC_content,SequenceQCSet-method	FastQC-class
Per_sequence_quality_scores	FastQC-class
Per_sequence_quality_scores,FastQC-method	FastQC-class
Per_sequence_quality_scores,SequenceQC-method	FastQC-class
Per_sequence_quality_scores,SequenceQCSet-method	FastQC-class
plotClusters	plotClusters
plotClusters,data.frame-method	plotClusters
plotClusters,GRanges-method	plotClusters
plotQdnaByCN	plotQdnaByCN
priorTab	BayMethList-class
priorTab,BayMethList-method	BayMethList-class
priorTab<-	BayMethList-class
priorTab<-,BayMethList-method	BayMethList-class
processNDF	processNDF
profilePlots	profilePlots
profilePlots,ScoresList-method	profilePlots
QdnaData	QdnaData
QdnaData-class	QdnaData
readFastQC	FastQC-class
regions	ChromaResults-class
regions,ChromaResults-method	ChromaResults-class
regionStats	regionStats
regionStats,AffymetrixCelSet-method	regionStats
regionStats,matrix-method	regionStats
RegionStats-class	regionStats
relativeCN	relativeCN
relativeCN,data.frame,matrix-method	relativeCN
relativeCN,GRanges,matrix-method	relativeCN
sampleInterest	BayMethList-class
sampleInterest,BayMethList-method	BayMethList-class
sampleInterest<-	BayMethList-class
sampleInterest<-,BayMethList-method	BayMethList-class
samplesList	samplesList
ScoresList	ScoresList-class
ScoresList-class	ScoresList-class
sequenceCalc	sequenceCalc
sequenceCalc,data.frame,BSgenome-method	sequenceCalc
sequenceCalc,GRanges,BSgenome-method	sequenceCalc
SequenceQC-class	FastQC-class
SequenceQCSet	FastQC-class
SequenceQCSet-class	FastQC-class
Sequence_Duplication_Levels	FastQC-class
Sequence_Duplication_Levels,FastQC-method	FastQC-class
Sequence_Duplication_Levels,SequenceQC-method	FastQC-class
Sequence_Duplication_Levels,SequenceQCSet-method	FastQC-class
Sequence_Length_Distribution	FastQC-class
Sequence_Length_Distribution,FastQC-method	FastQC-class
Sequence_Length_Distribution,SequenceQC-method	FastQC-class
Sequence_Length_Distribution,SequenceQCSet-method	FastQC-class
setCNVOffsets	setCNVOffsets
show,AdjustedCopyEstimate-method	AdjustedCopyEstimate-class
show,BayMethList-method	BayMethList-class
show,ChromaResults-method	ChromaResults-class
show,ClusteredScoresList-method	ClusteredScoresList-class
show,CopyEstimate-method	CopyEstimate-class
show,FastQC-method	FastQC-class
show,QdnaData-method	QdnaData
show,RegionStats-method	regionStats
show,ScoresList-method	ScoresList-class
show,SequenceQC-method	FastQC-class
show,SequenceQCSet-method	FastQC-class
subsetRows	ScoresList-class
subsetRows,ClusteredScoresList-method	ClusteredScoresList-class
subsetRows,ScoresList-method	ScoresList-class
summarizeScores	summarizeScores
summarizeScores,ScoresList,matrix-method	summarizeScores
tables	ScoresList-class
tables,ScoresList-method	ScoresList-class
windows	BayMethList-class
windows,BayMethList-method	BayMethList-class
windows<-	BayMethList-class
windows<-,BayMethList-method	BayMethList-class
writeWig	writeWig
writeWig,AffymetrixCelSet-method	writeWig
writeWig,GRangesList-method	writeWig
[,BayMethList,ANY,missing,ANY-method	BayMethList-class
[,ClusteredScoresList,ANY,missing,ANY-method	ClusteredScoresList-class
[,ScoresList,ANY,missing,ANY-method	ScoresList-class
[,SequenceQCSet,ANY,missing,ANY-method	FastQC-class
