| ChIPQC-package | ChIPQC - Quality metrics for ChIPseq data |
| averagepeaksignal | Retrieve average peak profiles |
| averagepeaksignal-method | Retrieve average peak profiles |
| averagepeaksignal-methods | Retrieve average peak profiles |
| blacklist_hg19 | Example data sets for 'ChIPQC' package, each containing a 'ChIPQCexperiment' object, as well as a pre-compiled blacklist for hg19. |
| 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 |
| 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. |
| example_QCexperiment | Example data sets for 'ChIPQC' package, each containing a 'ChIPQCexperiment' object, as well as a pre-compiled blacklist for hg19. |
| 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 |
| mapped | Retrieve numbers of mapped reads |
| mapped-method | Retrieve numbers of mapped reads |
| mapped-methods | Retrieve numbers of mapped reads |
| Normalisedaveragepeaksignal | Retrieve normalised average peak profiles |
| Normalisedaveragepeaksignal-method | Retrieve normalised average peak profiles |
| Normalisedaveragepeaksignal-methods | Retrieve normalised average peak profiles |
| 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 |
| 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 |
| 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 |
| 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 |
| tamoxifen_QC | Example data sets for 'ChIPQC' package, each containing a 'ChIPQCexperiment' object, as well as a pre-compiled blacklist for hg19. |