CGHbase: CGHbase: Base functions and classes for arrayCGH data analysis.

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Contains functions and classes that are needed by arrayCGH packages.

Author
Sjoerd Vosse, Mark van de Wiel
Date of publication
None
Maintainer
Mark van de Wiel <mark.vdwiel@vumc.nl>
License
GPL
Version
1.34.0
URLs

View on Bioconductor

Man pages

avedist
Retrieve regions information from cghRegions object.
CGHbase-package
CGHbase: Base functions and classes for arrayCGH data...
chromosomes
Retrieve feature position data from cgh objects.
class.cghCall
Class to contain and describe called array comparative...
class.cghRaw
Class to contain and describe raw or normalized array...
class.cghRegions
Class to contain and describe array comparative genomic...
class.cghSeg
Class to contain and describe segmented array comparative...
copynumber
Retrieve copynumber data from cgh objects.
frequencyPlot
Visualization of aCGH regions.
frequencyPlotCalls
Visualization of aCGH profiles.
make_cghRaw
Convert a dataframe or textfile to an object of class cghRaw.
plot
Plot aCGH data.
probloss
Retrieve call probabilities from a cghCall object.
regions
Retrieve regions data from cghRegions object.
summaryPlot
Visualization of aCGH profiles.
Wilting
Cervical cancer arrayCGH data
WiltingCalled
Cervical cancer arrayCGH data called with CGHcall
WiltingNorm
Normalized log2 ratios from cervical cancer arrayCGH data.
WiltingRaw
Raw log2 ratios from cervical cancer arrayCGH data.
WiltingRegions
Regions of cervical cancer arrayCGH data as defined by...
WiltingSeg
Segmented log2 ratios from cervical cancer arrayCGH data.

Files in this package

CGHbase/DESCRIPTION
CGHbase/NAMESPACE
CGHbase/R
CGHbase/R/allGeneric.R
CGHbase/R/classes.R
CGHbase/R/methods-cghCall.R
CGHbase/R/methods-cghRaw.R
CGHbase/R/methods-cghRegions.R
CGHbase/R/methods-cghSeg.R
CGHbase/R/private.R
CGHbase/R/tools.R
CGHbase/data
CGHbase/data/Wilting.txt
CGHbase/data/WiltingCalled.rda
CGHbase/data/WiltingNorm.rda
CGHbase/data/WiltingRaw.rda
CGHbase/data/WiltingRegions.rda
CGHbase/data/WiltingSeg.rda
CGHbase/data/datalist
CGHbase/man
CGHbase/man/CGHbase-package.Rd
CGHbase/man/Wilting.Rd
CGHbase/man/WiltingCalled.Rd
CGHbase/man/WiltingNorm.Rd
CGHbase/man/WiltingRaw.Rd
CGHbase/man/WiltingRegions.Rd
CGHbase/man/WiltingSeg.Rd
CGHbase/man/avedist.Rd
CGHbase/man/chromosomes.Rd
CGHbase/man/class.cghCall.Rd
CGHbase/man/class.cghRaw.Rd
CGHbase/man/class.cghRegions.Rd
CGHbase/man/class.cghSeg.Rd
CGHbase/man/copynumber.Rd
CGHbase/man/frequencyPlot.Rd
CGHbase/man/frequencyPlotCalls.Rd
CGHbase/man/make_cghRaw.Rd
CGHbase/man/plot.Rd
CGHbase/man/probloss.Rd
CGHbase/man/regions.Rd
CGHbase/man/summaryPlot.Rd