Comprehensive Pipeline for Analyzing and Visualizing Array-Based
CGH Data
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Documentation for package ‘rCGH’ version 1.37.0
Help Pages
| rCGH-package | Comprehensive Pipeline for Analyzing and Visualizing Array-Based CGH Data |
| Accessors | '"rCGH"' Accessor Functions |
| adjustSignal | Array-based CGH Preprocessing |
| adjustSignal-method | Array-based CGH Preprocessing |
| adjustSignal-methods | Array-based CGH Preprocessing |
| agilentDB | aCGH Agilent Probes GC Fraction |
| AllAccessors | '"rCGH"' Accessor Functions |
| byGeneTable | Converting a Segmentation Table Into a By-Gene Table |
| EMnormalize | Genomic Profile Centralization |
| EMnormalize-method | Genomic Profile Centralization |
| EMnormalize-methods | Genomic Profile Centralization |
| getCNset | '"rCGH"' Accessor Functions |
| getCNset-method | '"rCGH"' Accessor Functions |
| getCNset-methods | '"rCGH"' Accessor Functions |
| getInfo | '"rCGH"' Accessor Functions |
| getInfo-method | '"rCGH"' Accessor Functions |
| getInfo-methods | '"rCGH"' Accessor Functions |
| getParam | '"rCGH"' Accessor Functions |
| getParam-method | '"rCGH"' Accessor Functions |
| getParam-methods | '"rCGH"' Accessor Functions |
| getSegTable | '"rCGH"' Accessor Functions |
| getSegTable-method | '"rCGH"' Accessor Functions |
| getSegTable-methods | '"rCGH"' Accessor Functions |
| hg18 | Hg18 Chromosome Lengths and Centromere Locations |
| hg19 | Hg19 Chromosome Lengths and Centromere Locations |
| hg38 | Hg38 Chromosome Lengths and Centromere Locations |
| multiplot | Static Genomic Profile and LOH Visualization |
| multiplot-method | Static Genomic Profile and LOH Visualization |
| multiplot-methods | Static Genomic Profile and LOH Visualization |
| plotDensity | Visualizing the Log2Ratios Density and Centralization Decision |
| plotDensity-method | Visualizing the Log2Ratios Density and Centralization Decision |
| plotDensity-methods | Visualizing the Log2Ratios Density and Centralization Decision |
| plotLOH | Allelic Differences Visualization |
| plotLOH-method | Allelic Differences Visualization |
| plotLOH-methods | Allelic Differences Visualization |
| plotProfile | Static Genomic Profile Visualization |
| plotProfile-method | Static Genomic Profile Visualization |
| plotProfile-methods | Static Genomic Profile Visualization |
| rCGH | Comprehensive Pipeline for Analyzing and Visualizing Array-Based CGH Data |
| rCGH-Agilent-class | Class '"rCGH-Agilent"' |
| rCGH-class | Class '"rCGH"' |
| rCGH-cytoScan-class | Class '"rCGH-cytoScan"' |
| rCGH-generic-class | Class '"rCGH-generic"' |
| rCGH-oncoScan-class | Class '"rCGH-oncoScan"' |
| rCGH-SNP6-class | Class '"rCGH-SNP6"' |
| readAffyCytoScan | Affymetrix CytoScanHD '"rCGH-cytoScan"' Constructor |
| readAffyOncoScan | Affymetrix OncoScan '"rCGH-oncoScan"' Constructor |
| readAffySNP6 | Affymetrix SNP6 '"rCGH-SNP6"' Constructor |
| readAgilent | Agilent Dual-Color Hybridization '"rCGH-Agilent"' Constructor. |
| readGeneric | Generic rCGH object '"rCGH-generic"' Constructor |
| recenter | Recentering a Genomic Profile |
| recenter<- | Recentering a Genomic Profile |
| recenter<--method | Recentering a Genomic Profile |
| recenter<--methods | Recentering a Genomic Profile |
| segmentCGH | Genomic Profile Segmentation |
| segmentCGH-method | Genomic Profile Segmentation |
| segmentCGH-methods | Genomic Profile Segmentation |
| setInfo | Adding Information In An Object Of Class '"rCGH"' |
| setInfo<- | Adding Information In An Object Of Class '"rCGH"' |
| setInfo<--method | Adding Information In An Object Of Class '"rCGH"' |
| setInfo<--methods | Adding Information In An Object Of Class '"rCGH"' |
| show-method | 'show' '"rCGH"' |
| show-methods | 'show' '"rCGH"' |
| view | Interactive Genomic Profile Visualization |
| view-method | Interactive Genomic Profile Visualization |
| view-methods | Interactive Genomic Profile Visualization |