rCGH: Comprehensive Pipeline for Analyzing and Visualizing Array-Based CGH Data
Version 1.6.0

A comprehensive pipeline for analyzing and interactively visualizing genomic profiles generated through commercial or custom aCGH arrays. As inputs, rCGH supports Agilent dual-color Feature Extraction files (.txt), from 44 to 400K, Affymetrix SNP6.0 and cytoScanHD probeset.txt, cychp.txt, and cnchp.txt files exported from ChAS or Affymetrix Power Tools. rCGH also supports custom arrays, provided data complies with the expected format. This package takes over all the steps required for individual genomic profiles analysis, from reading files to profiles segmentation and gene annotations. This package also provides several visualization functions (static or interactive) which facilitate individual profiles interpretation. Input files can be in compressed format, e.g. .bz2 or .gz.

Browse man pages Browse package API and functions Browse package files

AuthorFrederic Commo [aut, cre]
Bioconductor views CopyNumberVariation FeatureExtraction Preprocessing aCGH
Date of publicationNone
MaintainerFrederic Commo <fredcommo@gmail.com>
LicenseArtistic-2.0
Version1.6.0
URL https://github.com/fredcommo/rCGH
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("rCGH")

Man pages

adjustSignal: 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
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
plotDensity: Visualizing the Log2Ratios Density and Centralization...
plotLOH: Allelic Differences Visualization
plotProfile: Static Genomic Profile Visualization
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-package: Comprehensive Pipeline for Analyzing and Visualizing...
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"'...
readGeneric: Generic rCGH object '"rCGH-generic"' Constructor
recenter: Recentering a Genomic Profile
segmentCGH: Genomic Profile Segmentation
setInfo: Adding Information In An Object Of Class '"rCGH"'
show-methods: 'show' '"rCGH"'
view: Interactive Genomic Profile Visualization

Functions

Accessors Man page
AllAccessors Man page
ByGene Source code
CyAdjust Source code
EMnormalize Man page
EMnormalize,rCGH-method Man page
EMnormalize-methods Man page
GCadjust Source code
MAD Source code
addDens Source code
addGenomeLoc Source code
addSegments Source code
addTagToPlot Source code
adjustSignal Man page
adjustSignal,rCGH-method Man page
adjustSignal-methods Man page
agilentDB Man page
byGeneTable Man page Source code
bygeneToSegValues Source code
chrAsNum Source code
cmValues Source code
computeMedSegm Source code
computeSegmentation Source code
convertLoc Source code
createGeneDB Source code
curateAgilentCnSet Source code
dlrs Source code
estimateCopy Source code
estimateRatio Source code
getCNset Man page
getCNset,rCGH-method Man page
getCNset-methods Man page
getCloser Source code
getGFlags Source code
getGenesFromSeg Source code
getInfo Man page
getInfo,rCGH-method Man page
getInfo-methods Man page
getMAD Source code
getParam Man page
getParam,rCGH-method Man page
getParam-methods Man page
getPatientId Source code
getRFlags Source code
getSegFromGene Source code
getSegLen Source code
getSegTable Man page
getSegTable,rCGH-method Man page
getSegTable-methods Man page
getTagValue Source code
hg18 Man page
hg19 Man page
hg38 Man page
locateCM Source code
mainPlot Source code
makeTitle Source code
medFlag Source code
mergeLevels Source code
mergePeaks Source code
mergeSegments Source code
modelLOH Source code
modelLR Source code
modelSignal Source code
multiplot Man page
multiplot,rCGH-method Man page
multiplot-methods Man page
onAttach Source code
plotCopy Source code
plotDensity Man page
plotDensity,rCGH-method Man page
plotDensity-methods Man page
plotLOH Man page
plotLOH,rCGH-method Man page
plotLOH-methods Man page
plotProfile Man page
plotProfile,rCGH-method Man page
plotProfile-methods Man page
preset Source code
probeCopyValue Source code
probeSegValue Source code
rCGH Man page
rCGH-Agilent-class Man page
rCGH-SNP6-class Man page
rCGH-class Man page
rCGH-cytoScan-class Man page
rCGH-generic-class Man page
rCGH-oncoScan-class Man page
rCGH-package Man page
readAffyCytoScan Man page Source code
readAffyOncoScan Man page Source code
readAffySNP6 Man page Source code
readAgilent Man page Source code
readAgilentInfo Source code
readAgilentMatrix Source code
readCytoScan Source code
readCytoScanMatrix Source code
readGeneric Man page Source code Source code
readSNP6 Source code
readSNP6Matrix Source code
recenter Man page
recenter<- Man page
recenter<-,rCGH-method Man page
recenter<--methods Man page
relativeLog Source code
renameChr Source code
renameGeneList Source code
replaceFlags Source code
segmentCGH Man page
segmentCGH,rCGH-method Man page
segmentCGH-methods Man page
setCores Source code
setInfo Man page
setInfo<- Man page
setInfo<-,rCGH-method Man page
setInfo<--methods Man page
show,rCGH-method Man page
show-methods Man page
simulateLRfromST Source code
smoothSeg Source code
suppressDuplic Source code
suppressDuplicLocs Source code
suppressDuplicProbes Source code
suppressFlags Source code
validAgilent Source code
validCytoScan Source code
validSNP6 Source code
validrCGHObject Source code
view Man page
view,rCGH-method Man page
view-methods Man page

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/AllClasses.R
R/AllGenerics.R
R/AllHelperFunctions.R
R/AllMethods.R
R/AllSetters.R
R/buildData.R
R/plotFunctions.R
R/zzz.R
build
build/vignette.rds
data
data/agilentDB_400K_GC.rda
data/datalist
data/hg18.rda
data/hg19.rda
data/hg38.rda
inst
inst/doc
inst/doc/rCGH.R
inst/doc/rCGH.Rnw
inst/doc/rCGH.pdf
inst/extdata
inst/extdata/Affy_cytoScan.cyhd.CN5.CNCHP.txt.bz2
inst/extdata/Affy_snp6_cnchp.txt.bz2
inst/extdata/Agilent4x180K.txt.bz2
inst/extdata/generic.txt.bz2
inst/extdata/oncoscan.tsv.bz2
inst/shinyProfile
inst/shinyProfile/data
inst/shinyProfile/data/empty.txt
inst/shinyProfile/helpers.R
inst/shinyProfile/server.R
inst/shinyProfile/ui.R
inst/shinyProfile/www
inst/shinyProfile/www/style.css
inst/unitTests
inst/unitTests/test_rCGH.R
man
man/AllAccessors.Rd
man/EMnormalize.Rd
man/adjustSignal.Rd
man/agilentDB.Rd
man/byGeneTable.Rd
man/hg18.Rd
man/hg19.Rd
man/hg38.Rd
man/multiplot.Rd
man/plotDensity.Rd
man/plotLOH.Rd
man/plotProfile.Rd
man/rCGH-Agilent-class.Rd
man/rCGH-SNP6-class.Rd
man/rCGH-class.Rd
man/rCGH-cytoScan-class.Rd
man/rCGH-generic-class.Rd
man/rCGH-oncoScan-class.Rd
man/rCGH-package.Rd
man/readAffyCytoScan.Rd
man/readAffyOncoScan.Rd
man/readAffySNP6.Rd
man/readAgilent.Rd
man/readGeneric.Rd
man/recenter.Rd
man/segmentCGH.Rd
man/setInfo.Rd
man/show-methods.Rd
man/view.Rd
tests
tests/runTests.R
vignettes
vignettes/rCGH.Rnw
vignettes/view.png
vignettes/workflowOverview.pdf
rCGH documentation built on May 20, 2017, 10:23 p.m.