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 |

http://www.stat.berkeley.edu/~johann/ruv |

**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

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
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