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

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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.

Author
Frederic Commo [aut, cre]
Date of publication
None
Maintainer
Frederic Commo <frederic.commo@gustaveroussy.fr>
License
Artistic-2.0
Version
1.4.0
URLs

View on Bioconductor

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

Files in this package

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