Learn R Programming

copynumber (version 1.12.0)

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

Description

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.

Copy Link

Version

Version

1.12.0

License

Artistic-2.0

Maintainer

Gro Nilsen

Last Published

February 15th, 2017

Functions in copynumber (1.12.0)

winsorize

Winsorization of copy number data
pcfPlain

Plain single-sample copy number segmentation.
pcf

Single-sample copy number segmentation.
plotHeatmap

Plot copy number heatmap
plotFreq

Plot percentage of samples with an aberration at a genomic position
callAberrations

Call aberrations in segmented data
selectSegments

Select multipcf segments
plotAllele

Plot SNP data and/or aspcf segmentation results
SNPdata

Artificial SNP array data
aspcf

Allele-specific copy number segmentation.
plotSample

Plot copy number data and/or segmentation results by sample
interpolate.pcf

Interpolation of pcf-estimates.
subsetData

Retrieve a data subset
imputeMissing

Impute missing copy number values
multipcf

Multi-sample copy number segmentation.
getGRangesFormat

Get segments on the GRanges format
plotGenome

Plot copy number data and/or segmentation results
plotChrom

Plot copy number data and/or segmentation results by chromosome
subsetSegments

Retrieve a subset of segments
plotGamma

Plot segmentation results for several values of gamma
micma

Subset of 244K aCGH data
lymphoma

3K aCGH data
plotAberration

Plot areas with copy number aberrations
plotCircle

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