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

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

Author
Maria Ortiz [aut, ctb], Ander Aramburu [ctb], Henrik Bengtsson [aut, cre, cph], Pierre Neuvial [aut, ctb], Angel Rubio [aut, ctb]
Date of publication
2015-10-27 08:09:53
Maintainer
Henrik Bengtsson <henrikb@braju.com>
License
LGPL (>= 2.1)
Version
0.12.1
URLs

View on CRAN

Man pages

calmateByThetaAB.array
Normalize allele-specific copy numbers (CA,CB)
calmateByTotalAndFracB.array
Normalize allele-specific copy numbers (total,fracB)
CalMaTeCalibration
The CalMaTeCalibration class
calmate-package
Package calmate
fitCalMaTeCNprobes.matrix
Normalizes non-polymorphic copy number loci according to the...
fitCalMaTeInternal
Algorithms to fit the CalMaTe model for a single SNP
fitCalMaTe.matrix
Calibrates SNP loci according to the CalMaTe method
Non-documented_objects
Non-documented objects
thetaAB2TotalAndFracB.array
Converts an Jx2xI array between (thetaA,thetaB) and...

Files in this package

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