Package: ruv 0.9.7.1

ruv: Detect and Remove Unwanted Variation using Negative Controls

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 in Gagnon-Bartsch and Speed (2012) <doi:10.1093/nar/gkz433>, Gagnon-Bartsch, Jacob and Speed (2013), and Molania, et. al. (2019) <doi:10.1093/nar/gkz433>. 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', 'RUV-rinv', 'RUV-I', and RUV-III', along with various supporting algorithms.

Authors:Johann Gagnon-Bartsch <[email protected]>

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34 exports 2 stars 2.73 score 29 dependencies 10 dependents 4 mentions 94 scripts 1.9k downloads

Last updated 5 years agofrom:992316897d. Checks:OK: 4 NOTE: 5. Indexed: yes.

Exports:collapse.replicatesdesign.matrixget_empirical_variancesgetKgoogle_searchinputcheck1invvarprojectionplotvariablesrandinvvarreplicate.matrixresidopruv_cancorplotruv_ecdfruv_histruv_projectionplotruv_rankplotruv_residualsruv_rleruv_screeruv_shinyruv_summaryruv_svdgridplotruv_svdplotruv_varianceplotruv_volcanoRUV1RUV2RUV4RUVIRUVIIIRUVinvRUVrinvsigmashrinkvariance_adjust

Dependencies:clicolorspacefansifarverggplot2gluegridExtragtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigR6RColorBrewerrlangscalestibbleutf8vctrsviridisLitewithr