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copynumber

Segmentation of single- and multi-track copy number data by penalized least squares regression.

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.

Functions (24)

Artificial SNP array data

Allele-specific copy number segmentation.

callAberrations

Call aberrations in segmented data

getGRangesFormat

Get segments on the GRanges format

imputeMissing

Impute missing copy number values

interpolate.pcf

Interpolation of pcf-estimates.

3K aCGH data

Subset of 244K aCGH data

Multi-sample copy number segmentation.

pcf

Single-sample copy number segmentation.

Plain single-sample copy number segmentation.

plotAberration

Plot areas with copy number aberrations

Plot SNP data and/or aspcf segmentation results

Plot copy number data and/or segmentation results by chromosome

Plot a circular genome with aberration frequencies and connections between genomic loci added.

Plot percentage of samples with an aberration at a genomic position

Plot segmentation results for several values of gamma

Plot copy number data and/or segmentation results

plotHeatmap

Plot copy number heatmap

Plot copy number data and/or segmentation results by sample

selectSegments

Select multipcf segments

Retrieve a data subset

subsetSegments

Retrieve a subset of segments

Winsorization of copy number data

copynumber

Segmentation of single- and multi-track copy number data by penalized least squares regression.

v1.30.0

Artistic-2.0

Authors

Gro Nilsen, Knut Liestoel and Ole Christian Lingjaerde.

Initial release

2013-04-16

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