collapse.replicates

The replicate structure. See <code><a rd-options="" href="/link/RUVIII?package=ruv&version=0.9.7.1" data-mini-rdoc="ruv::RUVIII">RUVIII</a></code> for details.

This function is intended for use in conjunction with <code>RUVIII</code>, specifically when using the <code>average=TRUE</code> option. When using the <code>average=TRUE</code> option, the adjusted data matrix has only one row for each set of replicates. In other words, each set of replicate rows in the orginal data matrix is "collapsed" into a single row in the adjusted data matrix. This function similarly collapses the rows of a dataframe of covariates. Only covariates that are constant within each set of replicates are retained.

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

collapse.replicates function

<dl> <dt>df</dt>
<dd>A dataframe.</dd> <dt>M</dt>
<dd>The replicate structure. See <code>RUVIII</code> for details.</dd>
</dl>

Arguments

Johann Gagnon-Bartsch <a href="/link/johanngb%40umich.edu?package=ruv&version=0.9.7.1" data-mini-rdoc="ruv::johanngb@umich.edu">johanngb@umich.edu</a>

Author

Collapse Replicates — collapse.replicates

<dl>

 <dt>df</dt>
<dd>A dataframe.</dd>

 <dt>M</dt>
<dd>The replicate structure. See <code>RUVIII</code> for details.</dd>


</dl>

Johann Gagnon-Bartsch <a href='mailto:johanngb@umich.edu'>johanngb@umich.edu</a>

collapse.replicates: Collapse Replicates

Description

Usage

Value

Arguments

Author

See Also