copynumber: Segmentation of single- and multi-track copy number data by penalized least squares regression.
Version 1.16.0

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.

Browse man pages Browse package API and functions Browse package files

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
Version1.16.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("copynumber")

Man pages

aspcf: 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.
lymphoma: 3K aCGH data
micma: Subset of 244K aCGH data
multipcf: Multi-sample copy number segmentation.
pcf: Single-sample copy number segmentation.
pcfPlain: Plain single-sample copy number segmentation.
plotAberration: Plot areas with copy number aberrations
plotAllele: Plot SNP data and/or aspcf segmentation results
plotChrom: Plot copy number data and/or segmentation results by...
plotCircle: Plot a circular genome with aberration frequencies and...
plotFreq: Plot percentage of samples with an aberration at a genomic...
plotGamma: Plot segmentation results for several values of gamma
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
selectSegments: Select multipcf segments
SNPdata: Artificial SNP array data
subsetData: Retrieve a data subset
subsetSegments: Retrieve a subset of segments
winsorize: Winsorization of copy number data

Functions

BAF Man page
PottsCompact Source code
addArmlines Source code
addChromlines Source code
addToFreqPlot Source code
addToPlot Source code
adjustPos Source code
adjustSeg Source code
adjustSegPos Source code
aspcf Man page Source code
aspcfpart Source code
c.lines Source code
callAberrations Man page Source code
checkAndRetrievePlotInput Source code
checkChrom Source code
checkSampleID Source code
checkSegments Source code
checkWinsoutliers Source code
chromMax Source code
chromPattern Source code
chromosomeAberration Source code
chromosomeFreq Source code
chromosomeHeat Source code
circ Source code
colorSetup Source code
compact Source code
compactMulti Source code
connectSeg Source code
convert.unit Source code
doMultiPCF Source code
draw.roundEdge Source code
drawStalk Source code
exactPcf Source code
expandMulti Source code
fastAspcf Source code
filterMarkS4 Source code
findEst Source code
findMarks Source code
findMarksMulti Source code
findNN Source code
framedim Source code
genomeAberration Source code
genomeFreq Source code
genomeHeat Source code
get.seglim Source code
get.xticks Source code
get.yticks Source code
getArmandChromStop Source code
getArms Source code
getCol Source code
getCumBin Source code
getFilename Source code
getFreqData Source code
getFreqPlotParameters Source code
getGRangesFormat Man page Source code
getGlobPos Source code
getGlobal.xlim Source code
getHeatParameters Source code
getMad Source code
getPlotParameters Source code
getPlotSymbols Source code
getUnisegFormat Source code
getx Source code
handleMissing Source code
imp.constant Source code
imp.pcf Source code
imputeMissing Man page Source code
interpolate.pcf Man page Source code
is.multiseg Source code
logR Man page
lymphoma Man page
madWins Source code
markMultiPotts Source code
markWithPotts Source code
medianFilter Source code
micma Man page
multiPCFcompact Source code
multipcf Man page Source code
numericArms Source code
numericChrom Source code
pcf Man page Source code
pcfPlain Man page Source code
pcfWins Source code
plotAberration Man page Source code
plotAllele Man page Source code
plotChrom Man page Source code
plotCircle Man page Source code
plotFreq Man page Source code
plotGamma Man page Source code
plotGenome Man page Source code
plotHeatmap Man page Source code
plotIdeogram Source code
plotObs Source code
plotSample Man page Source code
plotSegments Source code
psi Source code
pullOutContent Source code
runFastMultiPCF Source code
runFastPcf Source code
runMultiPcfSubset Source code
runPcfSubset Source code
sawMarkM Source code
selectFastMultiPcf Source code
selectFastPcf Source code
selectSegments Man page Source code
separateChrom Source code
subset.abe Source code
subset.length Source code
subset.var Source code
subsetData Man page Source code
subsetSegments Man page Source code
updateFreqParameters Source code
updatePlotParameters Source code
winsorize Man page Source code

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
copynumber documentation built on May 20, 2017, 11:01 p.m.