Quality metrics for ChIPseq data

Documentation for package ‘ChIPQC’ version 1.44.0

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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 --

exampleExp	Example data sets for 'ChIPQC' package, each containing a 'ChIPQCexperiment' object, as well as a pre-compiled blacklist for hg19.
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' object associated with an experiment
QCdba-method	Retrieve the 'DBA-object' object associated with an experiment
QCdba-methods	Retrieve the 'DBA-object' 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	Example data sets for 'ChIPQC' package, each containing a 'ChIPQCexperiment' object, as well as a pre-compiled blacklist for hg19.
tamoxifen_QC	Example data sets for 'ChIPQC' package, each containing a 'ChIPQCexperiment' object, as well as a pre-compiled blacklist for hg19.