CGH Micro-Array NORmalization
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Documentation for package ‘MANOR’ version 1.81.0
Help Pages
| amplicon.flag | Examples of flag objects to apply to CGH arrays |
| arrayTrend | Spatial trend of microarray spots statistic |
| arrayTrend.arrayCGH | Spatial trend of microarray spots statistic |
| arrayTrend.default | Spatial trend of microarray spots statistic |
| chromosome.flag | Examples of flag objects to apply to CGH arrays |
| clone.qscore | Examples of qscore objects (quality scores) to apply to CGH arrays |
| control.flag | Examples of flag objects to apply to CGH arrays |
| dapi.snr.flag | Examples of flag objects to apply to CGH arrays |
| detectSB | Spatial bias detection |
| detectSB.arrayCGH | Spatial bias detection |
| detectSB.default | Spatial bias detection |
| dyn.x.qscore | Examples of qscore objects (quality scores) to apply to CGH arrays |
| dyn.y.qscore | Examples of qscore objects (quality scores) to apply to CGH arrays |
| dynamics.qscore | Examples of qscore objects (quality scores) to apply to CGH arrays |
| edge | Examples of array-CGH data with spatial artifacts |
| edge.norm | Examples of array-CGH data with spatial artifacts |
| edge.txt | Examples of array-CGH data with spatial artifacts |
| flag | Apply a flag to an arrayCGH |
| flag.arrayCGH | Apply a flag to an arrayCGH |
| flag.summary | Summarize information about flags after array normalization |
| flag.summary.arrayCGH | Summarize information about flags after array normalization |
| flag.summary.default | Summarize information about flags after array normalization |
| flags | Examples of flag objects to apply to CGH arrays |
| genome.plot | Pan-genomic representation of a normalized arrayCGH |
| genome.plot.arrayCGH | Pan-genomic representation of a normalized arrayCGH |
| genome.plot.default | Pan-genomic representation of a normalized arrayCGH |
| global.spatial.flag | Examples of flag objects to apply to CGH arrays |
| gradient | Examples of array-CGH data with spatial artifacts |
| gradient.gpr | Examples of array-CGH data with spatial artifacts |
| gradient.norm | Examples of array-CGH data with spatial artifacts |
| html.report | Generate an HTML report of array normalization |
| html.report.arrayCGH | Generate an HTML report of array normalization |
| html.report.default | Generate an HTML report of array normalization |
| import | Import raw file to an arrayCGH object |
| import.default.aux | Import raw file to an arrayCGH object |
| import.gpr.aux | Import raw file to an arrayCGH object |
| import.spot.aux | Import raw file to an arrayCGH object |
| intensity.flag | Examples of flag objects to apply to CGH arrays |
| local.spatial.flag | Examples of flag objects to apply to CGH arrays |
| MANOR | Normalize an object of type arrayCGH |
| manor | Normalize an object of type arrayCGH |
| nem | Spatial Classification by EM algorithm |
| nem.arrayCGH | Spatial Classification by EM algorithm |
| nem.default | Spatial Classification by EM algorithm |
| norm | Normalize an object of type arrayCGH |
| norm.arrayCGH | Normalize an object of type arrayCGH |
| pct.clone.qscore | Examples of qscore objects (quality scores) to apply to CGH arrays |
| pct.replicate.qscore | Examples of qscore objects (quality scores) to apply to CGH arrays |
| pct.spot.before.qscore | Examples of qscore objects (quality scores) to apply to CGH arrays |
| pct.spot.qscore | Examples of qscore objects (quality scores) to apply to CGH arrays |
| position.flag | Examples of flag objects to apply to CGH arrays |
| qscore | Create an object of type qscore |
| qscore.arrayCGH | arrayCGH quality score |
| qscore.summary | Compute quality scores for a given arrayCGH object |
| qscore.summary.arrayCGH | Compute quality scores for a given arrayCGH object |
| ref.snr.flag | Examples of flag objects to apply to CGH arrays |
| rep.flag | Examples of flag objects to apply to CGH arrays |
| replicate.flag | Examples of flag objects to apply to CGH arrays |
| report.plot | Array image and a genomic representation of a normalized arrayCGH |
| report.plot.arrayCGH | Array image and a genomic representation of a normalized arrayCGH |
| report.plot.default | Array image and a genomic representation of a normalized arrayCGH |
| smoothness.qscore | Examples of qscore objects (quality scores) to apply to CGH arrays |
| SNR.flag | Examples of flag objects to apply to CGH arrays |
| sort | Sorting for normalized arrayCGH objects |
| sort.arrayCGH | Sorting for normalized arrayCGH objects |
| spatial | Examples of array-CGH data with spatial artifacts |
| spatial.flag | Examples of flag objects to apply to CGH arrays |
| spot.flag | Examples of flag objects to apply to CGH arrays |
| to.flag | Create an object of type flag |
| to.qscore | Create an object of type qscore |
| unique.flag | Examples of flag objects to apply to CGH arrays |
| val.mark.flag | Examples of flag objects to apply to CGH arrays |
| var.replicate.qscore | Examples of qscore objects (quality scores) to apply to CGH arrays |