Man pages for shengqh/ChIPQC
Quality metrics for ChIPseq data
| 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... |
