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

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

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("CNTools")
AuthorJianhua Zhang
Bioconductor views CopyNumberVariation Microarray
Date of publicationNone
MaintainerJ. Zhang <jzhang@jimmy.harvard.edu>
LicenseLGPL
Version1.32.0

View on Bioconductor

Functions

CNSeg Man page
CNSeg-class Man page
diffBy Man page
diffBy,ANY-method Man page
diffBy-method Man page
diffBy,RS-method Man page
genefilter-methods Man page
genefilter,RS-method Man page
geneInfo Man page
getCor Man page
getCor,ANY-method Man page
getCor-method Man page
getCor,RS-method Man page
getDist Man page
getDist,ANY-method Man page
getDist-method Man page
getDist,RS-method Man page
getRS Man page
getRS,CNSeg-method Man page
getRS-method Man page
madFilter Man page
madFilter,ANY-method Man page
madFilter-method Man page
madFilter,RS-method Man page
rs Man page
rs<- Man page
RS-class Man page
rs<-,RS-method Man page
rs,RS-method Man page
sampleData Man page
segBy Man page
segBy,RS-method Man page
segList Man page
segList<- Man page
segList<-,CNSeg-method Man page
segList,CNSeg-method Man page
segList-method Man page
show,CNSeg-method Man page
show,RS-method Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

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