Detect and Remove Unwanted Variation using Negative Controls

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Documentation for package ‘ruv’ version 0.9.7.1

• DESCRIPTION file.

Help Pages

ruv-package	Detect and Remove Unwanted Variation using Negative Controls
collapse.replicates	Collapse Replicates
design.matrix	Design Matrix
getK	Get K
get_empirical_variances	Get empirical variances
google_search	Google Search URL
inputcheck1	Input Check One
invvar	Inverse Method Variances
projectionplotvariables	Projection Plot Variables
randinvvar	(Randomization) Inverse Method Variances
replicate.matrix	Replicate (Mapping) Matrix
residop	Residual Operator
ruv	Detect and Remove Unwanted Variation using Negative Controls
RUV1	RUV-I
RUV2	Remove Unwanted Variation, 2-step
RUV4	Remove Unwanted Variation, 4-step
RUVI	RUV-I
RUVIII	RUV-III
RUVinv	Remove Unwanted Variation, inverse method
RUVrinv	Remove Unwanted Variation, ridged inverse method
ruv_cancorplot	RUV Canonical Correlation Plot
ruv_ecdf	RUV P-value Empirical CDF Plot
ruv_hist	RUV P-value Histogram Plot
ruv_projectionplot	RUV Projection Plot
ruv_rankplot	RUV Rank Plot
ruv_residuals	RUV Residuals
ruv_rle	RUV RLE Plot
ruv_scree	RUV Scree Plot
ruv_shiny	RUV Shiny App
ruv_summary	RUV Summary
ruv_svdgridplot	RUV SVD Grid Plot
ruv_svdplot	RUV SVD Plot
ruv_varianceplot	RUV Variance Plot
ruv_volcano	RUV Volcano Plot
sigmashrink	Empirical Bayes shrinkage estimate of sigma^2
variance_adjust	Adjust Estimated Variances