Man pages for ChIPQC
Quality metrics for ChIPseq data

averagepeaksignal-methodsRetrieve average peak profiles
ChIPQCConstruct a 'ChIPQCexperiment' object
ChIPQC-dataExample data sets for 'ChIPQC' package, each containing a...
ChIPQCexperiment-classChIPQCexperiment instances
ChIPQC-packageChIPQC - Quality metrics for ChIPseq data
ChIPQCreportGenerate a summary QC report
ChIPQCsample-classClass '"ChIPQCsample"'
coveragehistogram-methodsRetrieve histogram data representing densities of coverage...
crosscoverage-methodsRetrieve the cross coverage values for a range of shift sizes
duplicateRate-methodsRetrieve duplication rates
duplicates-methodsRetrieve numbers of duplicate reads.
flagtagcounts-methodsRetrieve numbers of reads that pass various filters
FragmentLengthCrossCoverage-methodsRetrieve the cross coverage values when extending reads to...
fragmentlength-methodsRetrieve the estimated fragment length
frip-methodsRetrieve fraction of reads in peaks
mapped-methodsRetrieve numbers of mapped reads
Normalisedaveragepeaksignal-methodsRetrieve normalised average peak profiles
peaks-methodsRetrieve peaks
plotCC-methodsGenerate Cross-Coverage plots
plotCorHeatmap-methodsGenerate Correlation Heatmap for ChIP samples
plotCoverageHist-methodsGenerate coverage histogram plot
plotFribl-methodsGenerate fraction of reads in blacklist plot
plotFrip-methodsGenerate fraction of reads in peaks plot
plotPeakProfile-methodsGenerate peak profile plots
plotPrincomp-methodsGenerate Principal Components Analysis plot for ChIP samples
plotRap-methodsGenerate reads in peaks plot
plotRegi-methodsGenerate relative enrichment of genomic features plot
plotSSD-methodsGenerate SSD plot
QCannotation-methodsRetrieve an annotation description, or a processed annotation
QCcontrol-methodsRetrieve control objects associated with a sample
QCdba-methodsRetrieve the 'DBA' object associated with an experiment
QCmetadata-methodsRetrieve metadata associated with an experiment
QCmetrics-methodsRetrieve consolidated set of QC metrics
QCsample-methodsRetrieve sample objects associated with an experiment
ReadLengthCrossCoverage-methodsRetrieve the cross coverage values without extending reads
readlength-methodsRetrieve read length values
reads-methodsRetrieve numbers of reads
regi-methodsRetrieve genomic profile information
RelativeCrossCoverage-methodsRetrieve the relative cross coverage values for a range of...
ribl-methodsRetrieve numbers of reads overlapping blacklisted regions
rip-methodsRetrieve numbers of reads overlapping peaks
ssd-methodsRetrieve SSD (squared sum of deviations) values of peak...
ChIPQC documentation built on Nov. 8, 2020, 8:06 p.m.