Package: copynumber 1.29.0.9000

Gro Nilsen

copynumber: Segmentation of single- and multi-track copy number data by penalized least squares regression (with hg38 and mm10).

Penalized least squares regression is applied to fit piecewise constant curves to copy number data to locate genomic regions of constant copy number. Procedures are available for individual segmentation of each sample, joint segmentation of several samples and joint segmentation of the two data tracks from SNP-arrays. Several plotting functions are available for visualization of the data and the segmentation results.

Authors:Gro Nilsen, Knut Liestoel and Ole Christian Lingjaerde.

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NEWS

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

Peer review:

Bug tracker:https://github.com/igordot/copynumber/issues

Datasets:
  • BAF - Artificial SNP array data
  • logR - Artificial SNP array data
  • lymphoma - 3K aCGH data
  • micma - Subset of 244K aCGH data

On CRAN:

21 exports 14 stars 1.38 score 17 dependencies

Last updated 1 years agofrom:2e31d59f558d5e3e44215da2f612707791e3f030

Exports:aspcfcallAberrationsgetGRangesFormatimputeMissinginterpolate.pcfmultipcfpcfpcfPlainplotAberrationplotAlleleplotChromplotCircleplotFreqplotGammaplotGenomeplotHeatmapplotSampleselectSegmentssubsetDatasubsetSegmentswinsorize

Dependencies:askpassBiocGenericscurlGenomeInfoDbGenomeInfoDbDataGenomicRangeshttrIRangesjsonlitemimeopensslR6S4VectorssysUCSC.utilsXVectorzlibbioc