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"ChIPQC-deprecated", "title": "Deprecated functions in package 'ChIPQC'", "topics": [ "ChIPQC-deprecated" ] }, { "page": "ChIPQCexperiment-class", "title": "ChIPQCexperiment instances", "topics": [ "ChIPQCexperiment", "ChIPQCexperiment-class", "show,ChIPQCexperiment-method" ] }, { "page": "ChIPQCreport", "title": "Generate a summary QC report", "topics": [ "ChIPQCreport", "ChIPQCreport,ChIPQCexperiment-method", "ChIPQCreport,ChIPQCsample-method", "ChIPQCreport,list-method", "ChIPQCreport-methods" ] }, { "page": "ChIPQCsample-class", "title": "Class '\"ChIPQCsample\"'", "topics": [ "ChIPQCsample", "ChIPQCsample-class", "show,ChIPQCsample-method" ] }, { "page": "coveragehistogram-methods", "title": "Retrieve histogram data representing densities of coverage pileups", "topics": [ "coveragehistogram", "coveragehistogram,ChIPQCexperiment-method", "coveragehistogram,ChIPQCsample-method", "coveragehistogram,list-method", "coveragehistogram-methods" ] }, { "page": "crosscoverage-methods", "title": "Retrieve the cross coverage values for a range of shift sizes", "topics": [ "crosscoverage", "crosscoverage,ChIPQCexperiment-method", "crosscoverage,ChIPQCsample-method", "crosscoverage,list-method", "crosscoverage-methods" ] }, { "page": "duplicateRate-methods", "title": "Retrieve duplication rates", "topics": [ "duplicateRate", "duplicateRate,ChIPQCexperiment-method", "duplicateRate,ChIPQCsample-method", "duplicateRate,list-method", "duplicateRate-methods" ] }, { "page": "duplicates-methods", "title": "Retrieve numbers of duplicate reads.", "topics": [ "duplicates", "duplicates,ChIPQCexperiment-method", "duplicates,ChIPQCsample-method", "duplicates,list-method", "duplicates-methods" ] }, { "page": "flagtagcounts-methods", "title": "Retrieve numbers of reads that pass various filters", "topics": [ "flagtagcounts", "flagtagcounts,ChIPQCexperiment-method", "flagtagcounts,ChIPQCsample-method", "flagtagcounts,list-method", "flagtagcounts-methods" ] }, { "page": "fragmentlength-methods", "title": "Retrieve the estimated fragment length", "topics": [ "fragmentlength", "fragmentlength,ChIPQCexperiment-method", "fragmentlength,ChIPQCsample-method", "fragmentlength,list-method", "fragmentlength-methods" ] }, { "page": "frip-methods", "title": "Retrieve fraction of reads in peaks", "topics": [ "frip", "frip,ChIPQCexperiment-method", "frip,ChIPQCsample-method", "frip,list-method", "frip-methods" ] }, { "page": "mapped-methods", "title": "Retrieve numbers of mapped reads", "topics": [ "mapped", "mapped,ChIPQCexperiment-method", "mapped,ChIPQCsample-method", "mapped,list-method", "mapped-methods" ] }, { "page": "Normalisedaveragepeaksignal-methods", "title": "Retrieve normalised average peak profiles", "topics": [ "Normalisedaveragepeaksignal", "Normalisedaveragepeaksignal,ChIPQCexperiment-method", "Normalisedaveragepeaksignal,ChIPQCsample-method", "Normalisedaveragepeaksignal,list-method", "Normalisedaveragepeaksignal-methods" ] }, { "page": "peaks-methods", "title": "Retrieve peaks", "topics": [ "peaks", "peaks,ChIPQCexperiment-method", "peaks,ChIPQCsample-method", "peaks,list-method", "peaks-methods" ] }, { "page": "plotCC-methods", "title": "Generate Cross-Coverage plots", "topics": [ "plotCC", "plotCC,ChIPQCexperiment-method", "plotCC,ChIPQCsample-method", "plotCC,list-method", "plotCC-methods" ] }, { "page": "plotCorHeatmap-methods", "title": "Generate Correlation Heatmap for ChIP samples", "topics": [ "plotCorHeatmap", "plotCorHeatmap,ChIPQCexperiment-method", "plotCorHeatmap-methods" ] }, { "page": "plotCoverageHist-methods", "title": "Generate coverage histogram plot", "topics": [ "plotCoverageHist", "plotCoverageHist,ChIPQCexperiment-method", "plotCoverageHist,ChIPQCsample-method", "plotCoverageHist,list-method", "plotCoverageHist-methods" ] }, { "page": "plotFribl-methods", "title": "Generate fraction of reads in blacklist plot", "topics": [ "plotFribl", "plotFribl,ChIPQCexperiment-method", "plotFribl,ChIPQCsample-method", "plotFribl,list-method", "plotFribl-methods" ] }, { "page": "plotFrip-methods", "title": "Generate fraction of reads in peaks plot", "topics": [ "plotFrip", "plotFrip,ChIPQCexperiment-method", "plotFrip,ChIPQCsample-method", "plotFrip,list-method", "plotFrip-methods" ] }, { "page": "plotPeakProfile-methods", "title": "Generate peak profile plots", "topics": [ "plotPeakProfile", "plotPeakProfile,ChIPQCexperiment-method", "plotPeakProfile,ChIPQCsample-method", "plotPeakProfile,list-method", "plotPeakProfile-methods" ] }, { "page": "plotPrincomp-methods", "title": "Generate Principal Components Analysis plot for ChIP samples", "topics": [ "plotPrincomp", "plotPrincomp,ChIPQCexperiment-method", "plotPrincomp-methods" ] }, { "page": "plotRap-methods", "title": "Generate reads in peaks plot", "topics": [ "plotRap", "plotRap,ChIPQCexperiment-method", "plotRap,ChIPQCsample-method", "plotRap,list-method", "plotRap-methods" ] }, { "page": "plotRegi-methods", "title": "Generate relative enrichment of genomic features plot", "topics": [ "plotRegi", "plotRegi,ChIPQCexperiment-method", "plotRegi,ChIPQCsample-method", "plotRegi,list-method", "plotRegi-methods" ] }, { "page": "plotSSD-methods", "title": "Generate SSD plot", "topics": [ "plotSSD", "plotSSD,ChIPQCexperiment-method", "plotSSD,ChIPQCsample-method", "plotSSD,list-method", "plotSSD-methods" ] }, { "page": "QCannotation-methods", "title": "Retrieve an annotation description, or a processed annotation", "topics": [ "QCannotation", "QCannotation,ChIPQCexperiment-method", "QCannotation-methods" ] }, { "page": "QCcontrol-methods", "title": "Retrieve control objects associated with a sample", "topics": [ "QCcontrol", "QCcontrol,ChIPQCexperiment-method", "QCcontrol-methods" ] }, { "page": "QCdba-methods", "title": "Retrieve the 'DBA-object' object associated with an experiment", "topics": [ "QCdba", "QCdba,ChIPQCexperiment-method", "QCdba-methods" ] }, { "page": "QCmetadata-methods", "title": "Retrieve metadata associated with an experiment", "topics": [ "QCmetadata", "QCmetadata,ChIPQCexperiment-method", "QCmetadata,list-method", "QCmetadata-methods" ] }, { "page": "QCmetrics-methods", "title": "Retrieve consolidated set of QC metrics", "topics": [ "QCmetrics", "QCmetrics,ChIPQCexperiment-method", "QCmetrics,ChIPQCsample-method", "QCmetrics,list-method", "QCmetrics-methods" ] }, { "page": "QCsample-methods", "title": "Retrieve sample objects associated with an experiment", "topics": [ "QCsample", "QCsample,ChIPQCexperiment-method", "QCsample-methods" ] }, { "page": "readlength-methods", "title": "Retrieve read length values", "topics": [ "readlength", "readlength,ChIPQCexperiment-method", "readlength,ChIPQCsample-method", "readlength,list-method", "readlength-methods" ] }, { "page": "FragmentLengthCrossCoverage-methods", "title": "Retrieve the cross coverage values when extending reads to the optimal fragment length.", "topics": [ "FragmentLengthCrossCoverage", "FragmentLengthCrossCoverage,ChIPQCexperiment-method", "FragmentLengthCrossCoverage,ChIPQCsample-method", "FragmentLengthCrossCoverage,list-method", "FragmentLengthCrossCoverage-methods" ] }, { "page": "ReadLengthCrossCoverage-methods", "title": "Retrieve the cross coverage values without extending reads", "topics": [ "ReadLengthCrossCoverage", "ReadLengthCrossCoverage,ChIPQCexperiment-method", "ReadLengthCrossCoverage,ChIPQCsample-method", "ReadLengthCrossCoverage,list-method", "ReadLengthCrossCoverage-methods" ] }, { "page": "reads-methods", "title": "Retrieve numbers of reads", "topics": [ "reads", "reads,ChIPQCexperiment-method", "reads,ChIPQCsample-method", "reads,list-method", "reads-methods" ] }, { "page": "regi-methods", "title": "Retrieve genomic profile information", "topics": [ "regi", "regi,ChIPQCexperiment-method", "regi,ChIPQCsample-method", "regi,list-method", "regi-methods" ] }, { "page": "RelativeCrossCoverage-methods", "title": "Retrieve the relative cross coverage 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