Package: CNTools 1.63.0

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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CNTools.pdf |CNTools.html✨
CNTools/json (API)

# Install 'CNTools' in R:

install.packages('CNTools', repos = c('https://bioc.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-1.63.0(bioc 3.21)CNTools-1.62.0(bioc 3.20)

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

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5.30 score 1 packages 33 scripts 320 downloads 21 mentions 13 exports 48 dependencies

Last updated 2 months agofrom:05a59fd597. Checks:OK: 1 NOTE: 8. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 29 2024
R-4.5-win-x86_64	NOTE	Nov 29 2024
R-4.5-linux-x86_64	NOTE	Nov 29 2024
R-4.4-win-x86_64	NOTE	Nov 29 2024
R-4.4-mac-x86_64	NOTE	Nov 29 2024
R-4.4-mac-aarch64	NOTE	Nov 29 2024
R-4.3-win-x86_64	NOTE	Nov 29 2024
R-4.3-mac-x86_64	NOTE	Nov 29 2024
R-4.3-mac-aarch64	NOTE	Nov 29 2024

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 GenomeInfoDb GenomeInfoDbData glue httr IRanges jsonlite KEGGREST lattice lifecycle Matrix MatrixGenerics matrixStats memoise mime openssl pkgconfig plogr png R6 rlang RSQLite S4Vectors survival sys UCSC.utils vctrs XML xtable XVector zlibbioc

NCTools HowTo

Rendered fromHowTo.Rnwusingutils::Sweaveon Nov 29 2024.

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