CNTools: Convert segment data into a region by sample matrix to allow for other high level computational analyses.

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This package provides tools to convert the output of segmentation analysis using DNAcopy to a matrix structure with overlapping segments as rows and samples as columns so that other computational analyses can be applied to segmented data

Author
Jianhua Zhang
Date of publication
None
Maintainer
J. Zhang <jzhang@jimmy.harvard.edu>
License
LGPL
Version
1.30.0

View on Bioconductor

Man pages

CNSeg-class
Class "CNSeg" contains the output of DNACopy segmentation...
cor-methods
Method that extends the cor function of stats to handle...
diffBy-methods
A filter that filters out features that do not differ by a...
dist-methods
A method that extends the generic function dist to handle...
genefilter-methods
A method that filters feature based on reduced segment
getRS-methods
method that convert segment data into reduced segment matrix
madFilter-methods
Method that filters reduced segment matrix by the mean...
RS-class
Class "RS" contains the Reduced Segment data matrix derived...

Files in this package

CNTools/DESCRIPTION
CNTools/NAMESPACE
CNTools/R
CNTools/R/ClassDefination.R
CNTools/R/SupportingFunctions.R
CNTools/R/zzz.R
CNTools/build
CNTools/build/vignette.rds
CNTools/data
CNTools/data/geneInfo.rda
CNTools/data/sampleData.rda
CNTools/inst
CNTools/inst/doc
CNTools/inst/doc/HowTo.R
CNTools/inst/doc/HowTo.Rnw
CNTools/inst/doc/HowTo.pdf
CNTools/man
CNTools/man/CNSeg-class.Rd
CNTools/man/RS-class.Rd
CNTools/man/cor-methods.Rd
CNTools/man/diffBy-methods.Rd
CNTools/man/dist-methods.Rd
CNTools/man/genefilter-methods.Rd
CNTools/man/getRS-methods.Rd
CNTools/man/madFilter-methods.Rd
CNTools/src
CNTools/src/getratios.c
CNTools/vignettes
CNTools/vignettes/HowTo.Rnw
CNTools/vignettes/fig01.png
CNTools/vignettes/fig02.png