Comprehensive Pipeline for Analyzing and Visualizing Agilent and Affymetrix Array-Based CGH Data


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Documentation for package ‘rCGH’ version 1.0.2

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rCGH-package Comprehensive Pipeline for Analyzing and Visualizing Agilent and Affymetrix 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
geneDB Gene Annotations, in Hg19
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
hg19 Hg19 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 Agilent and Affymetrix Array-Based CGH Data
rCGH-Agilent-class Class '"rCGH-Agilent"'
rCGH-class Class '"rCGH"'
rCGH-cytoScan-class Class '"rCGH-cytoScan"'
rCGH-SNP6-class Class '"rCGH-SNP6"'
readAffyCytoScan Affymetrix CytoScanHD '"rCGH-cytoScan"' Constructor
readAffySNP6 Affymetrix SNP6 '"rCGH-SNP6"' Constructor
readAgilent Agilent Dual-Color Hybridization '"rCGH-Agilent"' 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