Quality metrics for ChIPseq data

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Documentation for package ‘ChIPQC’ version 1.24.0

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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.