ruv: Detect and Remove Unwanted Variation using Negative Controls
Version 0.9.6

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.

Browse man pages Browse package API and functions Browse package files

AuthorJohann Gagnon-Bartsch <johanngb@umich.edu>
Date of publication2015-07-18 17:00:34
MaintainerJohann Gagnon-Bartsch <johanngb@umich.edu>
LicenseGPL
Version0.9.6
URL http://www.stat.berkeley.edu/~johann/ruv
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("ruv")

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

Functions

RUV1 Man page Source code
RUV2 Man page Source code
RUV4 Man page Source code
RUVinv Man page Source code
RUVrinv Man page Source code
getK Man page Source code
getKcutoff Source code
get_empirical_variances Man page Source code
getsizeratios Source code
inputcheck1 Man page Source code
invvar Man page Source code
momentintegral Source code
randinvvar Man page Source code
residop Man page Source code
ruv Man page
ruv-package Man page
sigmashrink Man page Source code
variance_adjust Man page Source code

Files

src
src/sigmashrink.c
src/increasingreg.c
src/wipeout.c
src/getsizeratios.c
NAMESPACE
R
R/momentintegral.R
R/RUVinv.R
R/getKcutoff.R
R/invvar.R
R/RUV4.R
R/getK.R
R/getsizeratios.R
R/RUV1.R
R/inputcheck1.R
R/get_empirical_variances.R
R/sigmashrink.R
R/variance_adjust.R
R/RUV2.R
R/RUVrinv.R
R/randinvvar.R
R/residop.R
MD5
DESCRIPTION
man
man/variance_adjust.Rd
man/RUV2.Rd
man/RUVinv.Rd
man/inputcheck1.Rd
man/RUV4.Rd
man/residop.Rd
man/invvar.Rd
man/get_empirical_variances.Rd
man/ruv-package.Rd
man/RUV1.Rd
man/RUVrinv.Rd
man/getK.Rd
man/sigmashrink.Rd
man/randinvvar.Rd
ruv documentation built on May 19, 2017, 5:04 p.m.