ChIPQC                  Construct a 'ChIPQCexperiment' object
ChIPQC-package          ChIPQC - Quality metrics for ChIPseq data
ChIPQCexperiment-class
                        ChIPQCexperiment instances
ChIPQCreport-methods    Generate a summary QC report
ChIPQCsample-class      Class '"ChIPQCsample"'
FragmentLengthCrossCoverage
                        Retrieve the cross coverage values when
                        extending reads to the optimal fragment length.
Normalisedaveragepeaksignal-methods
                        Retrieve normalised average peak profiles
QCannotation-methods    Retrieve an annotation description, or a
                        processed annotation
QCcontrol-methods       Retrieve control objects associated with a
                        sample
QCdba-methods           Retrieve the 'DBA-object' object associated
                        with an experiment
QCmetadata-methods      Retrieve metadata associated with an experiment
QCmetrics-methods       Retrieve consolidated set of QC metrics
QCsample-methods        Retrieve sample objects associated with an
                        experiment
ReadLengthCrossCoverage
                        Retrieve the cross coverage values without
                        extending reads
RelativeCrossCoverage-methods
                        Retrieve the relative cross coverage values for
                        a range of shift sizes
averagepeaksignal-methods
                        Retrieve average peak profiles
coveragehistogram-methods
                        Retrieve histogram data representing densities
                        of coverage pileups
crosscoverage-methods   Retrieve the cross coverage values for a range
                        of shift sizes
duplicateRate-methods   Retrieve duplication rates
duplicates-methods      Retrieve numbers of duplicate reads.
exampleExp              Example data sets for 'ChIPQC' package, each
                        containing a 'ChIPQCexperiment' object, as well
                        as a pre-compiled blacklist for hg19.
flagtagcounts-methods   Retrieve numbers of reads that pass various
                        filters
fragmentlength-methods
                        Retrieve the estimated fragment length
frip-methods            Retrieve fraction of reads in peaks
mapped-methods          Retrieve numbers of mapped reads
peaks-methods           Retrieve peaks
plotCC-methods          Generate Cross-Coverage plots
plotCorHeatmap-methods
                        Generate Correlation Heatmap for ChIP samples
plotCoverageHist-methods
                        Generate coverage histogram plot
plotFribl-methods       Generate fraction of reads in blacklist plot
plotFrip-methods        Generate fraction of reads in peaks plot
plotPeakProfile-methods
                        Generate peak profile plots
plotPrincomp-methods    Generate Principal Components Analysis plot for
                        ChIP samples
plotRap-methods         Generate reads in peaks plot
plotRegi-methods        Generate relative enrichment of genomic
                        features plot
plotSSD-methods         Generate SSD plot
readlength-methods      Retrieve read length values
reads-methods           Retrieve numbers of reads
regi-methods            Retrieve genomic profile information
ribl-methods            Retrieve numbers of reads overlapping
                        blacklisted regions
rip-methods             Retrieve numbers of reads overlapping peaks
ssd-methods             Retrieve SSD (squared sum of deviations) values
                        of peak coverage
