# Comprehensive Pipeline for Analyzing and Visualizing Array-Based CGH Data

## Documentation for package ‘rCGH’ version 1.39.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## 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