# Quality metrics for ChIPseq data

## Documentation for package ‘ChIPQC’ version 1.2.2

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D E F M N P Q R S T

ChIPQC-package | ChIPQC - Quality metrics for ChIPseq data

## -- A --

averagepeaksignal | Retrieve average peak profiles
averagepeaksignal-method | Retrieve average peak profiles
averagepeaksignal-methods | Retrieve average peak profiles

## -- B --

blacklist_hg19 | Example data sets for 'ChIPQC' package, each containing a 'ChIPQCexperiment' object, as well as a pre-compiled blacklist for hg19.

## -- C --

ChIPQC | Construct a 'ChIPQCexperiment' object
ChIPQCexperiment | ChIPQCexperiment instances
ChIPQCexperiment-class | ChIPQCexperiment instances
ChIPQCreport | Generate a summary QC report
ChIPQCreport-method | Generate a summary QC report
ChIPQCreport-methods | Generate a summary QC report
ChIPQCsample | Class '"ChIPQCsample"'
ChIPQCsample-class | Class '"ChIPQCsample"'
coveragehistogram | Retrieve histogram data representing densities of coverage pileups
coveragehistogram-method | Retrieve histogram data representing densities of coverage pileups
coveragehistogram-methods | Retrieve histogram data representing densities of coverage pileups
crosscoverage | Retrieve the cross coverage values for a range of shift sizes
crosscoverage-method | Retrieve the cross coverage values for a range of shift sizes
crosscoverage-methods | Retrieve the cross coverage values for a range of shift sizes

## -- D --

duplicateRate | Retrieve duplication rates
duplicateRate-method | Retrieve duplication rates
duplicateRate-methods | Retrieve duplication rates
duplicates | Retrieve numbers of duplicate reads.
duplicates-method | Retrieve numbers of duplicate reads.
duplicates-methods | Retrieve numbers of duplicate reads.

## -- E --

example_QCexperiment | Example data sets for 'ChIPQC' package, each containing a 'ChIPQCexperiment' object, as well as a pre-compiled blacklist for hg19.

## -- F --

flagtagcounts | Retrieve numbers of reads that pass various filters
flagtagcounts-method | Retrieve numbers of reads that pass various filters
flagtagcounts-methods | Retrieve numbers of reads that pass various filters
fragmentlength | Retrieve the estimated fragment length
fragmentlength-method | Retrieve the estimated fragment length
fragmentlength-methods | Retrieve the estimated fragment length
FragmentLengthCrossCoverage | Retrieve the cross coverage values when extending reads to the optimal fragment length.
FragmentLengthCrossCoverage-method | Retrieve the cross coverage values when extending reads to the optimal fragment length.
FragmentLengthCrossCoverage-methods | Retrieve the cross coverage values when extending reads to the optimal fragment length.
frip | Retrieve fraction of reads in peaks
frip-method | Retrieve fraction of reads in peaks
frip-methods | Retrieve fraction of reads in peaks

## -- M --

mapped | Retrieve numbers of mapped reads
mapped-method | Retrieve numbers of mapped reads
mapped-methods | Retrieve numbers of mapped reads

## -- N --

Normalisedaveragepeaksignal | Retrieve normalised average peak profiles
Normalisedaveragepeaksignal-method | Retrieve normalised average peak profiles
Normalisedaveragepeaksignal-methods | Retrieve normalised average peak profiles

## -- P --

peaks | Retrieve peaks
peaks-method | Retrieve peaks
peaks-methods | Retrieve peaks
plotCC | Generate Cross-Coverage plots
plotCC-method | Generate Cross-Coverage plots
plotCC-methods | Generate Cross-Coverage plots
plotCorHeatmap | Generate Correlation Heatmap for ChIP samples
plotCorHeatmap-method | Generate Correlation Heatmap for ChIP samples
plotCorHeatmap-methods | Generate Correlation Heatmap for ChIP samples
plotCoverageHist | Generate coverage histogram plot
plotCoverageHist-method | Generate coverage histogram plot
plotCoverageHist-methods | Generate coverage histogram plot
plotFribl | Generate fraction of reads in blacklist plot
plotFribl-method | Generate fraction of reads in blacklist plot
plotFribl-methods | Generate fraction of reads in blacklist plot
plotFrip | Generate fraction of reads in peaks plot
plotFrip-method | Generate fraction of reads in peaks plot
plotFrip-methods | Generate fraction of reads in peaks plot
plotPeakProfile | Generate peak profile plots
plotPeakProfile-method | Generate peak profile plots
plotPeakProfile-methods | Generate peak profile plots
plotPrincomp | Generate Principal Components Analysis plot for ChIP samples
plotPrincomp-method | Generate Principal Components Analysis plot for ChIP samples
plotPrincomp-methods | Generate Principal Components Analysis plot for ChIP samples
plotRap | Generate reads in peaks plot
plotRap-method | Generate reads in peaks plot
plotRap-methods | Generate reads in peaks plot
plotRegi | Generate relative enrichment of genomic features plot
plotRegi-method | Generate relative enrichment of genomic features plot
plotRegi-methods | Generate relative enrichment of genomic features plot
plotSSD | Generate SSD plot
plotSSD-method | Generate SSD plot
plotSSD-methods | Generate SSD plot

## -- Q --

QCannotation | Retrieve an annotation description, or a processed annotation
QCannotation-method | Retrieve an annotation description, or a processed annotation
QCannotation-methods | Retrieve an annotation description, or a processed annotation
QCcontrol | Retrieve control objects associated with a sample
QCcontrol-method | Retrieve control objects associated with a sample
QCcontrol-methods | Retrieve control objects associated with a sample
QCdba | Retrieve the 'DBA' object associated with an experiment
QCdba-method | Retrieve the 'DBA' object associated with an experiment
QCdba-methods | Retrieve the 'DBA' object associated with an experiment
QCmetadata | Retrieve metadata associated with an experiment
QCmetadata-method | Retrieve metadata associated with an experiment
QCmetadata-methods | Retrieve metadata associated with an experiment
QCmetrics | Retrieve consolidated set of QC metrics
QCmetrics-method | Retrieve consolidated set of QC metrics
QCmetrics-methods | Retrieve consolidated set of QC metrics
QCsample | Retrieve sample objects associated with an experiment
QCsample-method | Retrieve sample objects associated with an experiment
QCsample-methods | Retrieve sample objects associated with an experiment

## -- R --

readlength | Retrieve read length values
readlength-method | Retrieve read length values
readlength-methods | Retrieve read length values
ReadLengthCrossCoverage | Retrieve the cross coverage values without extending reads
ReadLengthCrossCoverage-method | Retrieve the cross coverage values without extending reads
ReadLengthCrossCoverage-methods | Retrieve the cross coverage values without extending reads
reads | Retrieve numbers of reads
reads-method | Retrieve numbers of reads
reads-methods | Retrieve numbers of reads
regi | Retrieve genomic profile information
regi-method | Retrieve genomic profile information
regi-methods | Retrieve genomic profile information
RelativeCrossCoverage | Retrieve the relative cross coverage values for a range of shift sizes
RelativeCrossCoverage-method | Retrieve the relative cross coverage values for a range of shift sizes
RelativeCrossCoverage-methods | Retrieve the relative cross coverage values for a range of shift sizes
ribl | Retrieve numbers of reads overlapping blacklisted regions
ribl-method | Retrieve numbers of reads overlapping blacklisted regions
ribl-methods | Retrieve numbers of reads overlapping blacklisted regions
rip | Retrieve numbers of reads overlapping peaks
rip-method | Retrieve numbers of reads overlapping peaks
rip-methods | Retrieve numbers of reads overlapping peaks

## -- S --

show-method | ChIPQCexperiment instances
show-method | Class '"ChIPQCsample"'
ssd | Retrieve SSD (squared sum of deviations) values of peak coverage
ssd-method | Retrieve SSD (squared sum of deviations) values of peak coverage
ssd-methods | Retrieve SSD (squared sum of deviations) values of peak coverage

## -- T --

tamoxifen_QC | Example data sets for 'ChIPQC' package, each containing a 'ChIPQCexperiment' object, as well as a pre-compiled blacklist for hg19.