calmate: Improved Allele-Specific Copy Number of SNP Microarrays for Downstream Segmentation

A multi-array post-processing method of allele-specific copy-number estimates (ASCNs).

Install the latest version of this package by entering the following in R:
install.packages("calmate")
AuthorMaria Ortiz [aut, ctb], Ander Aramburu [ctb], Henrik Bengtsson [aut, cre, cph], Pierre Neuvial [aut, ctb], Angel Rubio [aut, ctb]
Bioconductor views CopyNumberVariants Genetics Microarray OneChannel SNP TwoChannel aCGH
Date of publication2015-10-27 08:09:53
MaintainerHenrik Bengtsson <henrikb@braju.com>
LicenseLGPL (>= 2.1)
Version0.12.1
https://github.com/HenrikBengtsson/calmate/

View on CRAN

Functions

allocateOutputDataSets Man page
allocateOutputDataSets.CalMaTeCalibration Man page
as.character.CalMaTeCalibration Man page
calmate Man page
calmateByThetaAB Man page
calmateByThetaAB.array Man page
calmateByTotalAndFracB Man page
calmateByTotalAndFracB.array Man page
CalMaTeCalibration Man page
calmate-package Man page
cat Man page
findUnitsTodo Man page
findUnitsTodo.CalMaTeCalibration Man page
fitCalMaTe Man page
fitCalMaTeCNprobes Man page
fitCalMaTeCNprobes.matrix Man page
fitCalMaTeInternal Man page
fitCalMaTe.matrix Man page
fitCalMaTeMedians Man page
fitCalMaTeV1 Man page
fitCalMaTeV2 Man page
getAsteriskTags Man page
getAsteriskTags.CalMaTeCalibration Man page
getDataSets Man page
getDataSets.CalMaTeCalibration Man page
getFullName Man page
getFullName.CalMaTeCalibration Man page
getInputDataSet Man page
getInputDataSet.CalMaTeCalibration Man page
getName.CalMaTeCalibration Man page
getOutputDataSet Man page
getOutputDataSet.CalMaTeCalibration Man page
getOutputDataSets Man page
getOutputDataSets.CalMaTeCalibration Man page
getParameters.CalMaTeCalibration Man page
getPath.CalMaTeCalibration Man page
getReferences Man page
getReferences.CalMaTeCalibration Man page
getRootPath Man page
getRootPath.CalMaTeCalibration Man page
getTags Man page
getTags.CalMaTeCalibration Man page
nbrOfFiles Man page
nbrOfFiles.CalMaTeCalibration Man page
Non-documented objects Man page
process Man page
process.CalMaTeCalibration Man page
setTags Man page
setTags.CalMaTeCalibration Man page
thetaAB2TotalAndFracB Man page
thetaAB2TotalAndFracB.array Man page
totalAndFracB2ThetaAB Man page
totalAndFracB2ThetaAB.array Man page
truncateFracB Man page
truncateFracB.array Man page
truncateFracB.matrix Man page
truncateThetaAB Man page
truncateThetaAB.array Man page
truncateThetaAB.matrix Man page

Files

inst
inst/exData
inst/exData/thetaAB,100x2x40.Rbin
inst/exData/oneSNPdata,2x40.Rbin
inst/exData/myASCNData.Rbin
inst/testScripts
inst/testScripts/widgets
inst/testScripts/widgets/CalMaTe
inst/testScripts/widgets/CalMaTe/Z02.plots,segments.R inst/testScripts/widgets/CalMaTe/001.include.R inst/testScripts/widgets/CalMaTe/A01.TCGA,CalMaTe.R
inst/testScripts/publications
inst/testScripts/publications/CalMaTe
inst/testScripts/publications/CalMaTe/Z02.plots,segments.R inst/testScripts/publications/CalMaTe/Z01.plots,byChromosome.R inst/testScripts/publications/CalMaTe/A02.TCGA,CalMaTe,plots.R inst/testScripts/publications/CalMaTe/B01.GSE12702,ASCRMAv2.R
inst/testScripts/publications/CalMaTe/000.README.txt
inst/testScripts/publications/CalMaTe/B02.GSE12702,CalMaTe.R inst/testScripts/publications/CalMaTe/A01.TCGA,CalMaTe.R inst/testScripts/publications/CalMaTe/Z03.plots,byUnits.R
inst/testScripts/system
inst/testScripts/system/chipTypes
inst/testScripts/system/chipTypes/Mapping250K_Nsp,Sty
inst/testScripts/system/chipTypes/Mapping250K_Nsp,Sty/20100620,CalMaTe.R inst/testScripts/system/chipTypes/Mapping250K_Nsp,Sty/20100518b,CalMaTe.R inst/testScripts/system/chipTypes/Mapping250K_Nsp,Sty/20100518a,CRMAv2.R
inst/testScripts/system/chipTypes/Mapping10K_Xba142
inst/testScripts/system/chipTypes/Mapping10K_Xba142/20120206b,CalMaTe.R inst/testScripts/system/chipTypes/Mapping10K_Xba142/20120206a,CRMAv2.R
tests
tests/calmateByTotalAndFracB.R tests/thetaAB2TotalAndFracB.R tests/testScriptCalMaTe1.R tests/calmateByThetaAB.R
NAMESPACE
NEWS
R
R/000.R R/fitCalMaTe.R R/calmateByTotalAndFracB.R R/fitCalMaTeCNprobes.R R/CalMaTeCalibration.R R/thetaAB2TotalAndFracB.R R/fitCalMaTeMedians.R R/fitCalMaTeV2.R R/truncateFracB.R R/999.NonDocumentedObjects.R R/999.package.R R/fitCalMaTeInternal.R R/zzz.R R/calmateByThetaAB.R R/fitCalMaTeV1.R R/truncateThetaAB.R
MD5
DESCRIPTION
man
man/calmate-package.Rd man/fitCalMaTe.matrix.Rd man/calmateByTotalAndFracB.array.Rd man/CalMaTeCalibration.Rd man/fitCalMaTeInternal.Rd man/fitCalMaTeCNprobes.matrix.Rd man/thetaAB2TotalAndFracB.array.Rd man/calmateByThetaAB.array.Rd man/Non-documented_objects.Rd

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