Package: CNTools 1.68.0

J. Zhang

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

Authors:Jianhua Zhang

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manual.pdf |manual.html✨
card.svg |card.png
CNTools/json (API)

# Install 'CNTools' in R:

install.packages('CNTools', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

geneInfo - Method that convert segment data into reduced segment matrix
sampleData - Class "CNSeg" contains the output of DNACopy segmentation data that can be operated on by the associated methods

On BioConductor:CNTools-1.69.0(bioc 3.24)CNTools-1.68.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

microarray copynumbervariation

5.42 score 1 packages 44 scripts 21 mentions 13 exports 44 dependencies

Last updated from:cd975ed20b (on RELEASE_3_23). Checks:1 ERROR, 11 NOTE, 2 OK. Indexed: no.

Target	Result	Time
bioc-checks	ERROR	136
linux-devel-arm64	NOTE	209
linux-devel-x86_64	NOTE	221
source / vignettes	OK	185
linux-release-arm64	NOTE	184
linux-release-x86_64	NOTE	232
macos-release-arm64	NOTE	180
macos-release-x86_64	NOTE	357
macos-oldrel-arm64	NOTE	179
macos-oldrel-x86_64	NOTE	353
windows-devel	NOTE	179
windows-release	NOTE	165
windows-oldrel	NOTE	166
wasm-release	OK	117

Exports:CNSeg diffBy genefilter getCor getDist getRS madFilter rs rs<-segBy segList segList<-show

Dependencies:annotate AnnotationDbi askpass Biobase BiocGenerics Biostrings bit bit64 blob cachem cli cpp11 crayon curl DBI fastmap genefilter generics glue httr IRanges jsonlite KEGGREST lattice lifecycle Matrix MatrixGenerics matrixStats memoise mime openssl pkgconfig png R6 rlang RSQLite S4Vectors Seqinfo survival sys vctrs XML xtable XVector

NCTools HowTo

Rendered fromHowTo.Rnwusingutils::Sweaveon Jun 19 2026.

Last update: 2013-11-01
Started: 2013-11-01

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Class "CNSeg" contains the output of DNACopy segmentation data that can be operated on by the associated methods	CNSeg CNSeg-class sampleData segList segList,CNSeg-method segList-method segList<- segList<-,CNSeg-method show,CNSeg-method
A filter that filters out features that do not differ by a set threshold between a pair of samples	diffBy diffBy,ANY-method diffBy,RS-method diffBy-method
A method that extends the generic function dist to handle reduced segemnts	getDist getDist,ANY-method getDist,RS-method getDist-method
A method that filters feature based on reduced segment	genefilter,RS-method genefilter-methods
Method that extends the cor function of stats to handle reduced segment data	getCor getCor,ANY-method getCor,RS-method getCor-method
method that convert segment data into reduced segment matrix	geneInfo getRS getRS,CNSeg-method getRS-method
Method that filters reduced segment matrix by the mean absolute deviation	madFilter madFilter,ANY-method madFilter,RS-method madFilter-method
Class "RS" contains the Reduced Segment data matrix derived from the output of segmentation	rs rs,RS-method RS-class rs<- rs<-,RS-method segBy segBy,RS-method show,RS-method