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

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

Author
Maria Ortiz [aut], Henrik Bengtsson [aut, cre, cph], Angel Rubio [aut]
Date of publication
2015-10-27 08:09:51
Maintainer
Henrik Bengtsson <henrikb@braju.com>
License
LGPL (>= 2.1)
Version
0.8.1
URLs

View on CRAN

Man pages

ACNE-package
Package ACNE
doACNE
(ACNE)
fitSnpNmf
Non-negative matrix factorization (NMF) of a matrix...
fitSnpNmfArray
Allele-specific copy number estimation using non-negative...
NmfPlm
The NmfPlm class
NmfSnpPlm
The NmfSnpPlm class
Non-documented_objects
Non-documented objects
plot.SnpNmfFit
Generates a multi-panel plot summarizing the NMF SNP fit
pseudoinverse
Calculates the pseudo inverse of a matrix
removeOutliers
Removes outliers in matrix containing SNP signals
robustHInit
Robust initialization of the H (copy number) matrix
robustWInit
Robust initialization of the W (affinity) matrix
snpArrayToMatrix
Reshapes SNP data in matrix form to array form and vice versa
WHInit
Initialization of the W and H matrices

Files in this package

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