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

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.

AuthorFrederic Commo [aut, cre]
Date of publicationNone
MaintainerFrederic Commo <frederic.commo@gustaveroussy.fr>
LicenseArtistic-2.0
Version1.4.0
https://github.com/fredcommo/rCGH

View on Bioconductor

Functions

Accessors Man page
adjustSignal Man page
adjustSignal-methods Man page
adjustSignal,rCGH-method Man page
agilentDB Man page
AllAccessors Man page
byGeneTable Man page
EMnormalize Man page
EMnormalize-methods Man page
EMnormalize,rCGH-method Man page
getCNset Man page
getCNset-methods Man page
getCNset,rCGH-method Man page
getInfo Man page
getInfo-methods Man page
getInfo,rCGH-method Man page
getParam Man page
getParam-methods Man page
getParam,rCGH-method Man page
getSegTable Man page
getSegTable-methods Man page
getSegTable,rCGH-method Man page
hg18 Man page
hg19 Man page
hg38 Man page
multiplot Man page
multiplot-methods Man page
multiplot,rCGH-method Man page
plotDensity Man page
plotDensity-methods Man page
plotDensity,rCGH-method Man page
plotLOH Man page
plotLOH-methods Man page
plotLOH,rCGH-method Man page
plotProfile Man page
plotProfile-methods Man page
plotProfile,rCGH-method Man page
rCGH Man page
rCGH-Agilent-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
rCGH-SNP6-class Man page
readAffyCytoScan Man page
readAffyOncoScan Man page
readAffySNP6 Man page
readAgilent Man page
readGeneric Man page
recenter Man page
recenter<- Man page
recenter<--methods Man page
recenter<-,rCGH-method Man page
segmentCGH Man page
segmentCGH-methods Man page
segmentCGH,rCGH-method Man page
setInfo Man page
setInfo<- Man page
setInfo<--methods Man page
setInfo<-,rCGH-method Man page
show-methods Man page
show,rCGH-method Man page
view Man page
view-methods Man page
view,rCGH-method Man page

Files

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

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