Array CGH Data Analysis and Visualization

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Documentation for package ‘cghRA’ version 1.6.0

Help Pages 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"' class constructor Class '""'
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 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 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 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