RDocumentation
Moon
Learn R
Search all packages and functions
⚠️
There's a newer version (1.8.2) of this package.
Take me there.
ChIPQC (version 1.4.4)
Quality metrics for ChIPseq data
Description
Quality metrics for ChIPseq data
Copy Link
Copy
Link to current version
Version
Version
1.8.2
1.6.1
1.4.4
1.2.2
Down Chevron
Version
1.4.4
License
GPL (>= 3)
Maintainer
Tom Carroll
Last Published
January 1st, 1970
Functions in ChIPQC (1.4.4)
Search functions
frip-methods
Retrieve fraction of reads in peaks
ssd-methods
Retrieve SSD (squared sum of deviations) values of peak coverage
reads-methods
Retrieve numbers of reads
rip-methods
Retrieve numbers of reads overlapping peaks
mapped-methods
Retrieve numbers of mapped reads
regi-methods
Retrieve genomic profile information
averagepeaksignal-methods
Retrieve average peak profiles
plotFribl-methods
Generate fraction of reads in blacklist plot
plotCoverageHist-methods
Generate coverage histogram plot
ChIPQC-data
Example data sets for
ChIPQC
package, each containing a
ChIPQCexperiment
object, as well as a pre-compiled blacklist for hg19.
QCmetrics-methods
Retrieve consolidated set of QC metrics
ChIPQC
Construct a
ChIPQCexperiment
object
ChIPQC-package
ChIPQC - Quality metrics for ChIPseq data
plotPrincomp-methods
Generate Principal Components Analysis plot for ChIP samples
plotRap-methods
Generate reads in peaks plot
plotCorHeatmap-methods
Generate Correlation Heatmap for ChIP samples
plotCC-methods
Generate Cross-Coverage plots
ReadLengthReadLengthCrossCoverage-methods
Retrieve the cross coverage values without extending reads
readlength-methods
Retrieve read length values
QCsample-methods
Retrieve sample objects associated with an experiment
duplicateRate-methods
Retrieve duplication rates
crosscoverage-methods
Retrieve the cross coverage values for a range of shift sizes
fragmentlength-methods
Retrieve the estimated fragment length
ReadLengthFragmentLengthCrossCoverage-methods
Retrieve the cross coverage values when extending reads to the optimal fragment length.
plotRegi-methods
Generate relative enrichment of genomic features plot
plotSSD-methods
Generate SSD plot
RelativeCrossCoverage-methods
Retrieve the relative cross coverage values for a range of shift sizes
ribl-methods
Retrieve numbers of reads overlapping blacklisted regions
ChIPQCexperiment-class
ChIPQCexperiment instances
ChIPQCreport-methods
Generate a summary QC report
duplicates-methods
Retrieve numbers of duplicate reads.
QCannotation-methods
Retrieve an annotation description, or a processed annotation
flagtagcounts-methods
Retrieve numbers of reads that pass various filters
ChIPQCsample-class
Class
"ChIPQCsample"
coveragehistogram-methods
Retrieve histogram data representing densities of coverage pileups
QCcontrol-methods
Retrieve control objects associated with a sample
Normalisedaveragepeaksignal-methods
Retrieve normalised average peak profiles
plotFrip-methods
Generate fraction of reads in peaks plot
peaks-methods
Retrieve peaks
plotPeakProfile-methods
Generate peak profile plots
QCmetadata-methods
Retrieve metadata associated with an experiment
QCdba-methods
Retrieve the
DBA
object associated with an experiment