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

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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.

Author
Gro Nilsen, Knut Liestoel and Ole Christian Lingjaerde.
Date of publication
None
Maintainer
Gro Nilsen <gronilse@ifi.uio.no>
License
Artistic-2.0
Version
1.14.0

View on Bioconductor

Man pages

imputeMissing
Impute missing copy number values
plotChrom
Plot copy number data and/or segmentation results by...
plotFreq
Plot percentage of samples with an aberration at a genomic...
plotGenome
Plot copy number data and/or segmentation results
plotHeatmap
Plot copy number heatmap
plotSample
Plot copy number data and/or segmentation results by sample
subsetData
Retrieve a data subset
subsetSegments
Retrieve a subset of segments

Files in this package

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