ChIPQC: Quality metrics for ChIPseq data

Quality metrics for ChIPseq data.

AuthorTom Carroll, Wei Liu, Ines de Santiago, Rory Stark
Date of publicationNone
MaintainerTom Carroll <tc.infomatics@gmail.com>, Rory Stark <rory.stark@cruk.cam.ac.uk>
LicenseGPL (>= 3)
Version1.10.2

View on Bioconductor

Man pages

averagepeaksignal-methods: Retrieve average peak profiles

ChIPQC: Construct a 'ChIPQCexperiment' object

ChIPQC-data: Example data sets for 'ChIPQC' package, each containing a...

ChIPQCexperiment-class: ChIPQCexperiment instances

ChIPQC-package: ChIPQC - Quality metrics for ChIPseq data

ChIPQCreport: Generate a summary QC report

ChIPQCsample-class: Class '"ChIPQCsample"'

coveragehistogram-methods: Retrieve histogram data representing densities of coverage...

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.

flagtagcounts-methods: Retrieve numbers of reads that pass various filters

FragmentLengthCrossCoverage-methods: Retrieve the cross coverage values when extending reads to...

fragmentlength-methods: Retrieve the estimated fragment length

frip-methods: Retrieve fraction of reads in peaks

mapped-methods: Retrieve numbers of mapped reads

Normalisedaveragepeaksignal-methods: Retrieve normalised average peak profiles

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

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 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-methods: Retrieve the cross coverage values without extending reads

readlength-methods: Retrieve read length values

reads-methods: Retrieve numbers of reads

regi-methods: Retrieve genomic profile information

RelativeCrossCoverage-methods: Retrieve the relative cross coverage values for a range of...

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...

Functions

averagepeaksignal Man page
averagepeaksignal,ChIPQCexperiment-method Man page
averagepeaksignal,ChIPQCsample-method Man page
averagepeaksignal,list-method Man page
averagepeaksignal-methods Man page
blacklist_hg19 Man page
ChIPQC Man page
ChIPQCexperiment Man page
ChIPQCexperiment-class Man page
ChIPQC-package Man page
ChIPQCreport Man page
ChIPQCreport,ChIPQCexperiment-method Man page
ChIPQCreport,ChIPQCsample-method Man page
ChIPQCreport,list-method Man page
ChIPQCreport-methods Man page
ChIPQCsample Man page
ChIPQCsample-class Man page
coveragehistogram Man page
coveragehistogram,ChIPQCexperiment-method Man page
coveragehistogram,ChIPQCsample-method Man page
coveragehistogram,list-method Man page
coveragehistogram-methods Man page
crosscoverage Man page
crosscoverage,ChIPQCexperiment-method Man page
crosscoverage,ChIPQCsample-method Man page
crosscoverage,list-method Man page
crosscoverage-methods Man page
duplicateRate Man page
duplicateRate,ChIPQCexperiment-method Man page
duplicateRate,ChIPQCsample-method Man page
duplicateRate,list-method Man page
duplicateRate-methods Man page
duplicates Man page
duplicates,ChIPQCexperiment-method Man page
duplicates,ChIPQCsample-method Man page
duplicates,list-method Man page
duplicates-methods Man page
example_QCexperiment Man page
flagtagcounts Man page
flagtagcounts,ChIPQCexperiment-method Man page
flagtagcounts,ChIPQCsample-method Man page
flagtagcounts,list-method Man page
flagtagcounts-methods Man page
fragmentlength Man page
fragmentlength,ChIPQCexperiment-method Man page
fragmentlength,ChIPQCsample-method Man page
FragmentLengthCrossCoverage Man page
FragmentLengthCrossCoverage,ChIPQCexperiment-method Man page
FragmentLengthCrossCoverage,ChIPQCsample-method Man page
FragmentLengthCrossCoverage,list-method Man page
FragmentLengthCrossCoverage-methods Man page
fragmentlength,list-method Man page
fragmentlength-methods Man page
frip Man page
frip,ChIPQCexperiment-method Man page
frip,ChIPQCsample-method Man page
frip,list-method Man page
frip-methods Man page
mapped Man page
mapped,ChIPQCexperiment-method Man page
mapped,ChIPQCsample-method Man page
mapped,list-method Man page
mapped-methods Man page
Normalisedaveragepeaksignal Man page
Normalisedaveragepeaksignal,ChIPQCexperiment-method Man page
Normalisedaveragepeaksignal,ChIPQCsample-method Man page
Normalisedaveragepeaksignal,list-method Man page
Normalisedaveragepeaksignal-methods Man page
peaks Man page
peaks,ChIPQCexperiment-method Man page
peaks,ChIPQCsample-method Man page
peaks,list-method Man page
peaks-methods Man page
plotCC Man page
plotCC,ChIPQCexperiment-method Man page
plotCC,ChIPQCsample-method Man page
plotCC,list-method Man page
plotCC-methods Man page
plotCorHeatmap Man page
plotCorHeatmap,ChIPQCexperiment-method Man page
plotCorHeatmap-methods Man page
plotCoverageHist Man page
plotCoverageHist,ChIPQCexperiment-method Man page
plotCoverageHist,ChIPQCsample-method Man page
plotCoverageHist,list-method Man page
plotCoverageHist-methods Man page
plotFribl Man page
plotFribl,ChIPQCexperiment-method Man page
plotFribl,ChIPQCsample-method Man page
plotFribl,list-method Man page
plotFribl-methods Man page
plotFrip Man page
plotFrip,ChIPQCexperiment-method Man page
plotFrip,ChIPQCsample-method Man page
plotFrip,list-method Man page
plotFrip-methods Man page
plotPeakProfile Man page
plotPeakProfile,ChIPQCexperiment-method Man page
plotPeakProfile,ChIPQCsample-method Man page
plotPeakProfile,list-method Man page
plotPeakProfile-methods Man page
plotPrincomp Man page
plotPrincomp,ChIPQCexperiment-method Man page
plotPrincomp-methods Man page
plotRap Man page
plotRap,ChIPQCexperiment-method Man page
plotRap,ChIPQCsample-method Man page
plotRap,list-method Man page
plotRap-methods Man page
plotRegi Man page
plotRegi,ChIPQCexperiment-method Man page
plotRegi,ChIPQCsample-method Man page
plotRegi,list-method Man page
plotRegi-methods Man page
plotSSD Man page
plotSSD,ChIPQCexperiment-method Man page
plotSSD,ChIPQCsample-method Man page
plotSSD,list-method Man page
plotSSD-methods Man page
QCannotation Man page
QCannotation,ChIPQCexperiment-method Man page
QCannotation-methods Man page
QCcontrol Man page
QCcontrol,ChIPQCexperiment-method Man page
QCcontrol-methods Man page
QCdba Man page
QCdba,ChIPQCexperiment-method Man page
QCdba-methods Man page
QCmetadata Man page
QCmetadata,ChIPQCexperiment-method Man page
QCmetadata,list-method Man page
QCmetadata-methods Man page
QCmetrics Man page
QCmetrics,ChIPQCexperiment-method Man page
QCmetrics,ChIPQCsample-method Man page
QCmetrics,list-method Man page
QCmetrics-methods Man page
QCsample Man page
QCsample,ChIPQCexperiment-method Man page
QCsample-methods Man page
readlength Man page
readlength,ChIPQCexperiment-method Man page
readlength,ChIPQCsample-method Man page
ReadLengthCrossCoverage Man page
ReadLengthCrossCoverage,ChIPQCexperiment-method Man page
ReadLengthCrossCoverage,ChIPQCsample-method Man page
ReadLengthCrossCoverage,list-method Man page
ReadLengthCrossCoverage-methods Man page
readlength,list-method Man page
readlength-methods Man page
reads Man page
reads,ChIPQCexperiment-method Man page
reads,ChIPQCsample-method Man page
reads,list-method Man page
reads-methods Man page
regi Man page
regi,ChIPQCexperiment-method Man page
regi,ChIPQCsample-method Man page
regi,list-method Man page
regi-methods Man page
RelativeCrossCoverage Man page
RelativeCrossCoverage,ChIPQCexperiment-method Man page
RelativeCrossCoverage,ChIPQCsample-method Man page
RelativeCrossCoverage,list-method Man page
RelativeCrossCoverage-methods Man page
ribl Man page
ribl,ChIPQCexperiment-method Man page
ribl,ChIPQCsample-method Man page
ribl,list-method Man page
ribl-methods Man page
rip Man page
rip,ChIPQCexperiment-method Man page
rip,ChIPQCsample-method Man page
rip,list-method Man page
rip-methods Man page
show,ChIPQCexperiment-method Man page
show,ChIPQCsample-method Man page
ssd Man page
ssd,ChIPQCexperiment-method Man page
ssd,ChIPQCsample-method Man page
ssd,list-method Man page
ssd-methods Man page
tamoxifen_QC Man page

Files

ChIPQC/ChIPQC.Rproj
ChIPQC/DESCRIPTION
ChIPQC/NAMESPACE
ChIPQC/R
ChIPQC/R/ChIPQC_IF.R ChIPQC/R/ChIPQCexperiment-class.R ChIPQC/R/ChIPQCsample-class.R ChIPQC/R/dbaplots.R
ChIPQC/R/plots.r
ChIPQC/R/report.r
ChIPQC/R/sampleQC.R ChIPQC/R/utilities.R
ChIPQC/build
ChIPQC/build/vignette.rds
ChIPQC/data
ChIPQC/data/blacklist_hg19.RData
ChIPQC/data/datalist
ChIPQC/data/example_QCexperiment.RData
ChIPQC/data/tamoxifen_QC.RData
ChIPQC/inst
ChIPQC/inst/CITATION
ChIPQC/inst/NEWS.Rd
ChIPQC/inst/doc
ChIPQC/inst/doc/ChIPQC.R
ChIPQC/inst/doc/ChIPQC.Rnw
ChIPQC/inst/doc/ChIPQC.pdf
ChIPQC/inst/doc/ChIPQCSampleReport.pdf
ChIPQC/inst/doc/index.html
ChIPQC/inst/extdata
ChIPQC/inst/extdata/blacklist_hg19.bed
ChIPQC/inst/extdata/example_QCexperiment.csv
ChIPQC/inst/extdata/tamoxifenQC.csv
ChIPQC/man
ChIPQC/man/ChIPQC-data.Rd ChIPQC/man/ChIPQC-package.Rd ChIPQC/man/ChIPQC.Rd ChIPQC/man/ChIPQCexperiment-class.Rd ChIPQC/man/ChIPQCreport.Rd ChIPQC/man/ChIPQCsample-class.Rd ChIPQC/man/FragmentLengthCrossCoverage-methods.Rd ChIPQC/man/Normalisedaveragepeaksignal-methods.Rd ChIPQC/man/QCannotation-methods.Rd ChIPQC/man/QCcontrol-methods.Rd ChIPQC/man/QCdba-methods.Rd ChIPQC/man/QCmetadata-methods.Rd ChIPQC/man/QCmetrics-methods.Rd ChIPQC/man/QCsample-methods.Rd ChIPQC/man/ReadLengthCrossCoverage-methods.Rd ChIPQC/man/RelativeCrossCoverage-methods.Rd ChIPQC/man/averagepeaksignal-methods.Rd ChIPQC/man/coveragehistogram-methods.Rd ChIPQC/man/crosscoverage-methods.Rd ChIPQC/man/duplicateRate-methods.Rd ChIPQC/man/duplicates-methods.Rd ChIPQC/man/flagtagcounts-methods.Rd ChIPQC/man/fragmentlength-methods.Rd ChIPQC/man/frip-methods.Rd ChIPQC/man/mapped-methods.Rd ChIPQC/man/peaks-methods.Rd ChIPQC/man/plotCC-methods.Rd ChIPQC/man/plotCorHeatmap-methods.Rd ChIPQC/man/plotCoverageHist-methods.Rd ChIPQC/man/plotFribl-methods.Rd ChIPQC/man/plotFrip-methods.Rd ChIPQC/man/plotPeakProfile-methods.Rd ChIPQC/man/plotPrincomp-methods.Rd ChIPQC/man/plotRap-methods.Rd ChIPQC/man/plotRegi-methods.Rd ChIPQC/man/plotSSD-methods.Rd ChIPQC/man/readlength-methods.Rd ChIPQC/man/reads-methods.Rd ChIPQC/man/regi-methods.Rd ChIPQC/man/ribl-methods.Rd ChIPQC/man/rip-methods.Rd ChIPQC/man/ssd-methods.Rd
ChIPQC/vignettes
ChIPQC/vignettes/ChIPQC.Rnw
ChIPQC/vignettes/ChIPQC.bib

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

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