ruv: Detect and Remove Unwanted Variation using Negative Controls

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Implements the 'RUV' (Remove Unwanted Variation) algorithms. These algorithms attempt to adjust for systematic errors of unknown origin in high-dimensional data. The algorithms were originally developed for use with genomic data, especially microarray data, but may be useful with other types of high-dimensional data as well. These algorithms were proposed by Gagnon-Bartsch and Speed (2012), and by Gagnon-Bartsch, Jacob and Speed (2013). The algorithms require the user to specify a set of negative control variables, as described in the references. The algorithms included in this package are 'RUV-2', 'RUV-4', 'RUV-inv', and 'RUV-rinv', along with various supporting algorithms.

Author
Johann Gagnon-Bartsch <johanngb@umich.edu>
Date of publication
2015-07-18 17:00:34
Maintainer
Johann Gagnon-Bartsch <johanngb@umich.edu>
License
GPL
Version
0.9.6
URLs

View on CRAN

Man pages

get_empirical_variances
Get empirical variances
getK
Get K
inputcheck1
Input Check One
invvar
Inverse Method Variances
randinvvar
(Randomization) Inverse Method Variances
residop
Residual Operator
RUV1
RUV-1
RUV2
Remove Unwanted Variation, 2-step
RUV4
Remove Unwanted Variation, 4-step
RUVinv
Remove Unwanted Variation, inverse method
ruv-package
Detect and Remove Unwanted Variation using Negative Controls
RUVrinv
Remove Unwanted Variation, ridged inverse method
sigmashrink
Empirical Bayes shrinkage estimate of sigma^2
variance_adjust
Adjust Estimated Variances

Files in this package

ruv
ruv/src
ruv/src/sigmashrink.c
ruv/src/increasingreg.c
ruv/src/wipeout.c
ruv/src/getsizeratios.c
ruv/NAMESPACE
ruv/R
ruv/R/momentintegral.R
ruv/R/RUVinv.R
ruv/R/getKcutoff.R
ruv/R/invvar.R
ruv/R/RUV4.R
ruv/R/getK.R
ruv/R/getsizeratios.R
ruv/R/RUV1.R
ruv/R/inputcheck1.R
ruv/R/get_empirical_variances.R
ruv/R/sigmashrink.R
ruv/R/variance_adjust.R
ruv/R/RUV2.R
ruv/R/RUVrinv.R
ruv/R/randinvvar.R
ruv/R/residop.R
ruv/MD5
ruv/DESCRIPTION
ruv/man
ruv/man/variance_adjust.Rd
ruv/man/RUV2.Rd
ruv/man/RUVinv.Rd
ruv/man/inputcheck1.Rd
ruv/man/RUV4.Rd
ruv/man/residop.Rd
ruv/man/invvar.Rd
ruv/man/get_empirical_variances.Rd
ruv/man/ruv-package.Rd
ruv/man/RUV1.Rd
ruv/man/RUVrinv.Rd
ruv/man/getK.Rd
ruv/man/sigmashrink.Rd
ruv/man/randinvvar.Rd