Package: cghMCR 1.65.0

J. Zhang

cghMCR: Find chromosome regions showing common gains/losses

This package provides functions to identify genomic regions of interests based on segmented copy number data from multiple samples.

Authors:J. Zhang and B. Feng

cghMCR_1.65.0.tar.gz
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cghMCR.pdf |cghMCR.html✨
cghMCR/json (API)

# Install 'cghMCR' in R:
install.packages('cghMCR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:
  • segData - The constructor for the cghMCR class

On BioConductor:cghMCR-1.63.0(bioc 3.20)cghMCR-1.62.0(bioc 3.19)

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

microarraycopynumbervariation

3.30 score 1 scripts 324 downloads 7 exports 51 dependencies

Last updated 23 days agofrom:7280ca7187. Checks:OK: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-winWARNINGOct 30 2024
R-4.5-linuxWARNINGOct 30 2024
R-4.4-winWARNINGOct 30 2024
R-4.4-macWARNINGOct 30 2024
R-4.3-winWARNINGOct 30 2024
R-4.3-macWARNINGOct 30 2024

Exports:cghMCRgolMCRmergeMCRProbesplotplot.DNAcopySGOL

Dependencies:annotateAnnotationDbiaskpassBiobaseBiocGenericsBiostringsbitbit64blobcachemcliCNToolscpp11crayoncurlDBIDNAcopyfastmapgenefilterGenomeInfoDbGenomeInfoDbDatagluehttrIRangesjsonliteKEGGRESTlatticelifecyclelimmaMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpkgconfigplogrpngR6rlangRSQLiteS4VectorsstatmodsurvivalsysUCSC.utilsvctrsXMLxtableXVectorzlibbioc

cghMCR findMCR

Rendered fromfindMCR.Rnwusingutils::Sweaveon Oct 30 2024.

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

Readme and manuals

Help Manual

Help pageTopics
The constructor for the cghMCR classcghMCR segData
Class "cghMCR" is a S4 class for the identification of minimum common regions of gains or losses across samplescghMCR-class getSegments getSegments,marrayNorm-method getSegments,marrayRaw-method MCR MCR,cghMCR-method
Methods for Function colnames/rownames in Package `cghMCR'colnames,SGOL-method colnames-methods rownames,SGOL-method rownames-methods [,SGOL-method [-methods
A function that appends probe ids to a data frame containing MCRsmergeMCRProbes
A function to plot the original data along with the segments identified using segment of DNAcopy.plot.DNAcopy
Class "SGOL" reprents segments of gain or loss across samplesgol gol,SGOL-method method,SGOL-method plot plot,ANY-method plot,methods plot,SGOL,ANY-method plot,SGOL-method SGOL SGOL-class threshold,SGOL-method