# Array CGH Data Analysis and Visualization

## Documentation for package ‘cghRA’ version 1.6.0

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

## Help Pages

Agilent.design | Design file parser
Agilent.probes | Probe file parser
applyMap | Update a track coordinates to match a distinct CGH design
bias | WACA bias computation for a probe series
blatInstall | Localize CGH probes in a genome
cghRA.array | cghRA.array class constructor
cghRA.array-class | Class '"cghRA.array"'
cghRA.copies | cghRA.copies class constructor
cghRA.copies-class | Class '"cghRA.copies"'
cghRA.design | cghRA.design class constructor
cghRA.design-class | Class '"cghRA.design"'
cghRA.probes | cghRA.probes class constructor
cghRA.probes-class | Class '"cghRA.probes"'
cghRA.regions | cghRA.regions class constructor
cghRA.regions-class | Class '"cghRA.regions"'
cghRA.series | cghRA.series class constructor
cghRA.series-class | Class '"cghRA.series"'
cnvScore | Polymorphism likelihood score for a genomic segment
copies | LogRatio to copies conversion
custom.design | Design file parser
custom.probes | Probe file parser
Design file parser | Design file parser
drawableFromClass.cghRA.probes | Extend Rgb compatibility to cghRA.probes
fillGaps | Fill gaps between consecutive segments
GEDI | Gene Expression and Dosage Integrator
LCN | LogRatio to copies conversion
localize | Localize CGH probes in a genome
LRA | Short/Long Recurrent Abnormalities detection
map2design | Update a track coordinates to match a distinct CGH design
model.apply | Computes copy number for a set of CGH segments
model.auto | Automatic generation of copy number model
model.test | Copy number model quality assessment
parallelize | Reshapes a list of segments
parseKaryo | Parses a karyotype-like formula
penetrance | Penetrance computation from a series of segments
Probe file parser | Probe file parser
process | cghRA array processing
process.applyModel | cghRA array processing
process.core | cghRA array processing
process.default | cghRA array processing
process.export | cghRA array processing
process.fill | cghRA array processing
process.fittest | cghRA array processing
process.log | cghRA array processing
process.mask | cghRA array processing
process.modelize | cghRA array processing
process.parse | cghRA array processing
process.probes | cghRA array processing
process.regions | cghRA array processing
process.replicates | cghRA array processing
process.segment | cghRA array processing
process.spatial | cghRA array processing
process.waca | cghRA array processing
segmentMap-class | Class '"segmentMap"'
SRA | Short/Long Recurrent Abnormalities detection
STEPS | Selective Trends Evidenced by Penetrance Surge
tk.annotate | Interactive cghRA track annotation
tk.cghRA | cghRA Tcl-Tk launcher
tk.design | Interactive cghRA design processing
tk.modelize | Interactive copy number modelization
tk.process | cghRA array processing
tk.series | Interactive cghRA series processing
tk.value | Tk interface utilities
trace2track | Converts cnvScore traces to a drawable track
track.CNV.DGVsupp | DGV supporting variant parser
WACA | Waves aCGH Correction Algorithm
xRA | Short/Long Recurrent Abnormalities detection