ACNE: Affymetrix SNP Probe-Summarization using Non-Negative Matrix Factorization

A summarization method to estimate allele-specific copy number signals for Affymetrix SNP microarrays using non-negative matrix factorization (NMF).

Install the latest version of this package by entering the following in R:
install.packages("ACNE")
AuthorMaria Ortiz [aut], Henrik Bengtsson [aut, cre, cph], Angel Rubio [aut]
Bioconductor views CopyNumberVariants Genetics Microarray OneChannel SNP TwoChannel aCGH
Date of publication2015-10-27 08:09:51
MaintainerHenrik Bengtsson <henrikb@braju.com>
LicenseLGPL (>= 2.1)
Version0.8.1
https://github.com/HenrikBengtsson/ACNE

View on CRAN

Files

inst
inst/testScripts
inst/testScripts/system
inst/testScripts/system/chipTypes
inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240
inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/test20090128,50K,NMF.R inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/test20100517,50K,doACNE.R inst/testScripts/system/chipTypes/Mapping50K_Hind240,Xba240/test20090122,50K,NMF,freqB.R
inst/testScripts/system/chipTypes/Mapping250K_Nsp,Sty
inst/testScripts/system/chipTypes/Mapping250K_Nsp,Sty/test20090128,250K,TumorNormal,NMF.R inst/testScripts/system/chipTypes/Mapping250K_Nsp,Sty/test20100517,250K,doACNE.R
inst/testScripts/system/chipTypes/Mapping10K_Xba142
inst/testScripts/system/chipTypes/Mapping10K_Xba142/test20090128,10K,NMF.R inst/testScripts/system/chipTypes/Mapping10K_Xba142/test20100517,10K,doACNE.R
inst/extData
inst/extData/V4.Rbin
inst/extData/V5.Rbin
inst/extData/V6.Rbin
inst/extData/V1.Rbin
inst/extData/V3.Rbin
inst/extData/V2.Rbin
tests
tests/fitSnpNmfArray.R
NAMESPACE
NEWS
R
R/robustWInit.R R/000.R R/NmfSnpPlm.R R/fitSnpNmfArray.R R/WHInit.R R/snpArrayToMatrix.R R/miqr.solve.R R/pseudoinverse.R R/NmfPlm.R R/plotFreqB.R R/SnpNmfFit.plot.R R/doACNE.R R/999.NonDocumentedObjects.R R/999.package.R R/fitSnpNmf.R R/zzz.R R/removeOutliers.R R/robustHInit.R
MD5
DESCRIPTION
man
man/NmfPlm.Rd man/NmfSnpPlm.Rd man/fitSnpNmfArray.Rd man/robustWInit.Rd man/pseudoinverse.Rd man/WHInit.Rd man/fitSnpNmf.Rd man/robustHInit.Rd man/plot.SnpNmfFit.Rd man/ACNE-package.Rd man/doACNE.Rd man/removeOutliers.Rd man/snpArrayToMatrix.Rd man/Non-documented_objects.Rd

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