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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copynumber.pdf |copynumber.html✨
copynumber/json (API)
NEWS

# Install 'copynumber' in R:

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

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:

acgh snp copynumbervariation genetics visualization

3.85 score 18 stars 79 scripts 21 exports 18 dependencies

Last updated 2 years agofrom:2e31d59f55. Checks:OK: 1 NOTE: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 24 2024
R-4.5-win	NOTE	Nov 24 2024
R-4.5-linux	NOTE	Nov 24 2024
R-4.4-win	NOTE	Nov 24 2024
R-4.4-mac	NOTE	Nov 24 2024
R-4.3-win	NOTE	Nov 24 2024
R-4.3-mac	NOTE	Nov 24 2024

Exports:aspcf callAberrations getGRangesFormat imputeMissing interpolate.pcf multipcf pcf pcfPlain plotAberration plotAllele plotChrom plotCircle plotFreq plotGamma plotGenome plotHeatmap plotSample selectSegments subsetData subsetSegments winsorize

Dependencies:askpass BiocGenerics curl generics GenomeInfoDb GenomeInfoDbData GenomicRanges httr IRanges jsonlite mime openssl R6 S4Vectors sys UCSC.utils XVector zlibbioc

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Allele-specific copy number segmentation.	aspcf
Call aberrations in segmented data	callAberrations
Get segments on the GRanges format	getGRangesFormat
Impute missing copy number values	imputeMissing
Interpolation of pcf-estimates.	interpolate.pcf
3K aCGH data	lymphoma
Subset of 244K aCGH data	micma
Multi-sample copy number segmentation.	multipcf
Single-sample copy number segmentation.	pcf
Plain single-sample copy number segmentation.	pcfPlain
Plot areas with copy number aberrations	plotAberration
Plot SNP data and/or aspcf segmentation results	plotAllele
Plot copy number data and/or segmentation results by chromosome	plotChrom
Plot a circular genome with aberration frequencies and connections between genomic loci added.	plotCircle
Plot percentage of samples with an aberration at a genomic position	plotFreq
Plot segmentation results for several values of gamma	plotGamma
Plot copy number data and/or segmentation results	plotGenome
Plot copy number heatmap	plotHeatmap
Plot copy number data and/or segmentation results by sample	plotSample
Select multipcf segments	selectSegments
Artificial SNP array data	BAF logR
Retrieve a data subset	subsetData
Retrieve a subset of segments	subsetSegments
Winsorization of copy number data	winsorize