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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("copynumber")
AuthorGro Nilsen, Knut Liestoel and Ole Christian Lingjaerde.
Bioconductor views CopyNumberVariation Genetics SNP Visualization aCGH
Date of publicationNone
MaintainerGro Nilsen <gronilse@ifi.uio.no>
LicenseArtistic-2.0
Version1.14.0

View on Bioconductor

Files

DESCRIPTION
NAMESPACE
R
R/addArmlines.r R/addChromlines.r R/addToFreqPlot.r R/addToPlot.r R/adjustPos.r R/adjustSeg.r R/adjustSegPos.r R/aspcf.r R/callAberrations.r R/checkAndRetrievePlotInput.r R/checkChrom.r R/checkSampleID.r R/checkSegments.r R/checkWinsoutliers.r R/chromMax.r R/chromPattern.r R/colorSetup.r R/connectSeg.r R/convert_unit.r R/findNN.r R/framedim.r R/get.seglim.r R/getArmandChromStop.r R/getArms.r R/getCol.r R/getFilename.r R/getFreqData.r R/getFreqParameters.r R/getGRangesFormat.r R/getGlobPos.r R/getGlobal.xlim.r R/getHeatParameters.r R/getMad.r R/getPlotParameters.r R/getPlotSymbols.r R/getUnisegFormat.r R/get_xticks.r R/get_yticks.r R/getx.r R/handleMissing.r R/imputeMissing.R R/interpolate.pcf.r R/is_multiseg.r R/medianFilter.r R/multipcf.r R/numericArms.r R/numericChrom.r R/pcf.r R/pcfPlain.r R/plotAberration.r R/plotAllele.r R/plotChrom.r R/plotCircle.r R/plotFreq.r R/plotGamma.r R/plotGenome.r R/plotHeatmap.r R/plotIdeogram.r R/plotObs.r R/plotSample.r R/plotSegments.r R/pullOutContent.r R/selectSegments.r R/separateChrom.r R/subsetData.r R/subsetSegments.r
R/sysdata.rda
R/updateFreqParameters.r R/updatePlotParameters.r R/winsorize.r
build
build/vignette.rds
data
data/BAF.rda
data/logR.rda
data/lymphoma.rda
data/micma.rda
inst
inst/CITATION
inst/NEWS
inst/doc
inst/doc/copynumber.R
inst/doc/copynumber.pdf
inst/doc/copynumber.rnw
man
man/SNPdata.rd
man/aspcf.rd
man/callAberrations.rd
man/getGRangesFormat.rd
man/imputeMissing.Rd
man/interpolate.pcf.rd
man/lymphoma.rd
man/micma.rd
man/multipcf.rd
man/pcf.rd
man/pcfPlain.rd
man/plotAberration.rd
man/plotAllele.rd
man/plotChrom.Rd
man/plotCircle.rd
man/plotFreq.Rd
man/plotGamma.rd
man/plotGenome.Rd man/plotHeatmap.Rd man/plotSample.Rd
man/selectSegments.rd
man/subsetData.Rd man/subsetSegments.Rd
man/winsorize.rd
vignettes
vignettes/copynumber.rnw
vignettes/overview.pdf

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