ChIPQC: Quality metrics for ChIPseq data
Version 1.12.0

Quality metrics for ChIPseq data.

Browse man pages Browse package API and functions Browse package files

AuthorTom Carroll, Wei Liu, Ines de Santiago, Rory Stark
Bioconductor views ChIPSeq QualityControl ReportWriting Sequencing
Date of publicationNone
MaintainerTom Carroll <tc.infomatics@gmail.com>, Rory Stark <rory.stark@cruk.cam.ac.uk>
LicenseGPL (>= 3)
Version1.12.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("ChIPQC")

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

ChIPQC Man page Source code
ChIPQC-package Man page
ChIPQCexperiment Man page
ChIPQCexperiment-class 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 Source code
ChIPQCsample-class Man page
FragmentLengthCrossCoverage Man page
FragmentLengthCrossCoverage,ChIPQCexperiment-method Man page
FragmentLengthCrossCoverage,ChIPQCsample-method Man page
FragmentLengthCrossCoverage,list-method Man page
FragmentLengthCrossCoverage-methods Man page
GetGRanges Source code
Normalisedaveragepeaksignal Man page
Normalisedaveragepeaksignal,ChIPQCexperiment-method Man page
Normalisedaveragepeaksignal,ChIPQCsample-method Man page
Normalisedaveragepeaksignal,list-method Man page
Normalisedaveragepeaksignal-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
QCminimize Source code
QCsample Man page
QCsample,ChIPQCexperiment-method Man page
QCsample-methods Man page
ReadLengthCrossCoverage Man page
ReadLengthCrossCoverage,ChIPQCexperiment-method Man page
ReadLengthCrossCoverage,ChIPQCsample-method Man page
ReadLengthCrossCoverage,list-method Man page
ReadLengthCrossCoverage-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
RleSumAny Source code
addMatchingSample Source code
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
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
doChIPQCsample Source code
do_plotCorHeatmap Source code
do_plotPCA Source code
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
extend Source code
findCovMaxPos Source code
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
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
getAnnotation Source code
getAtts Source code
getMeta Source code
getMetaFor Source code
list2matrix Source code
listadd Source code
makeCCplot Source code
makeCoveragePlot Source code
makeFriblPlot Source code
makeFripPlot Source code
makeIntroduction Source code
makePeakProfilePlot Source code
makeRapPlot Source code
makeRegiPlot Source code
makeSSDPlot Source code
makeSummarySection Source code
mapped Man page
mapped,ChIPQCexperiment-method Man page
mapped,ChIPQCsample-method Man page
mapped,list-method Man page
mapped-methods Man page
mergeMetadata Source code
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
readlength Man page
readlength,ChIPQCexperiment-method Man page
readlength,ChIPQCsample-method 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
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
sampleQC Source code
show,ChIPQCexperiment-method Man page
show,ChIPQCsample-method Man page
showChIPQCexperiment Source code
ssd Man page
ssd,ChIPQCexperiment-method Man page
ssd,ChIPQCsample-method Man page
ssd,list-method Man page
ssd-methods Man page
table_RleList Source code
tamoxifen_QC Man page

Files

ChIPQC.Rproj
DESCRIPTION
NAMESPACE
R
R/ChIPQC_IF.R
R/ChIPQCexperiment-class.R
R/ChIPQCsample-class.R
R/dbaplots.R
R/plots.r
R/report.r
R/sampleQC.R
R/utilities.R
build
build/vignette.rds
data
data/blacklist_hg19.RData
data/datalist
data/example_QCexperiment.RData
data/tamoxifen_QC.RData
inst
inst/CITATION
inst/NEWS.Rd
inst/doc
inst/doc/ChIPQC.R
inst/doc/ChIPQC.Rnw
inst/doc/ChIPQC.pdf
inst/doc/ChIPQCSampleReport.pdf
inst/doc/index.html
inst/extdata
inst/extdata/blacklist_hg19.bed
inst/extdata/example_QCexperiment.csv
inst/extdata/tamoxifenQC.csv
man
man/ChIPQC-data.Rd
man/ChIPQC-package.Rd
man/ChIPQC.Rd
man/ChIPQCexperiment-class.Rd
man/ChIPQCreport.Rd
man/ChIPQCsample-class.Rd
man/FragmentLengthCrossCoverage-methods.Rd
man/Normalisedaveragepeaksignal-methods.Rd
man/QCannotation-methods.Rd
man/QCcontrol-methods.Rd
man/QCdba-methods.Rd
man/QCmetadata-methods.Rd
man/QCmetrics-methods.Rd
man/QCsample-methods.Rd
man/ReadLengthCrossCoverage-methods.Rd
man/RelativeCrossCoverage-methods.Rd
man/averagepeaksignal-methods.Rd
man/coveragehistogram-methods.Rd
man/crosscoverage-methods.Rd
man/duplicateRate-methods.Rd
man/duplicates-methods.Rd
man/flagtagcounts-methods.Rd
man/fragmentlength-methods.Rd
man/frip-methods.Rd
man/mapped-methods.Rd
man/peaks-methods.Rd
man/plotCC-methods.Rd
man/plotCorHeatmap-methods.Rd
man/plotCoverageHist-methods.Rd
man/plotFribl-methods.Rd
man/plotFrip-methods.Rd
man/plotPeakProfile-methods.Rd
man/plotPrincomp-methods.Rd
man/plotRap-methods.Rd
man/plotRegi-methods.Rd
man/plotSSD-methods.Rd
man/readlength-methods.Rd
man/reads-methods.Rd
man/regi-methods.Rd
man/ribl-methods.Rd
man/rip-methods.Rd
man/ssd-methods.Rd
vignettes
vignettes/ChIPQC.Rnw
vignettes/ChIPQC.bib
ChIPQC documentation built on May 20, 2017, 10:53 p.m.