CSresult-class

An S4 class in which the results of the Connectivity Scores by Factor Analysis are stored.

Applies factor analysis methodology to microarray data in order
to derive connectivity scores between compounds. The package also contains an
implementation of the connectivity score algorithm by Zhang and Gant (2008) <doi:10.1186/1471-2105-9-258>.

Ewoud Troyer

CSFA

Connectivity Scores with Factor Analysis

CSresult-class function

<dl class="dl-horizontal">
<dt><code>type</code></dt><dd>A character string containing the analysis type.</dd></dl><dt><code>CS</code></dt><dd>List of any number of lists (depending on how many components were selected) which contain the connectivity loadings and ranking scores for the reference (and query loadings). If permutation was applied, will also contain p-values.</dd><dt><code>GS</code></dt><dd>Dataframe containing the gene scores.</dd><dt><code>extra</code></dt><dd>List which contains <code>CSRank_Full</code> (contains all intermediate values while calculating the CS Ranking Score), <code>Object</code> (contains the complete original FA or Zhang result) and <code>samplefactorlabels</code> (contains thresholded labels based on the factor loadings, see plot <code>which=8</code>).</dd><dt><code>permutation.object</code></dt><dd>Contains CS for permuted data (matrix) and a dataframe with the p-values (only for MFA and Zhang).</dd><dt><code>call</code></dt><dd>List object containing the original call of <code>CSanalysis</code> as well as the parameters for the chosen method.</dd>

CSresult-class: An S4 class in which the results of the Connectivity Scores by Factor Analysis are stored.

Description

Arguments

Slots