ruv_volcano

The results of a call to <code><a rd-options="" href="/link/ruv_summary?package=ruv&version=0.9.7.1" data-mini-rdoc="ruv::ruv_summary">ruv_summary</a></code>.

Which column of the X matrix to make the plot for. Can be either an integer or a character string.

X.col

A scatter plot of negative log p-values against coefficient estimates, commonly known as a volcano plot

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.

Johann Gagnon-Bartsch

Detect and Remove Unwanted Variation using Negative Controls

ruv_volcano function

The results of a call to <code><a rd-options='' href='ruv_summary'>ruv_summary</a></code>.

ruv_volcano: RUV Volcano Plot

Description

Usage

Arguments

Value