pcaScoresFromLogFC

Perform principal component analysis and derive PCA scores from a logFC
matrix

Provides data structures and functions for data transformation and visualization in computational biology in drug discovery as part of the 'ribios' software suite. Zhang (2025) <https://github.com/bedapub/ribiosPlot>.

Jitao David Zhang

ribiosPlot

Plotting Module of the 'ribios' Software Suite

pcaScoresFromLogFC function

<dl><dt>lfcMat</dt>
<dd>Log fold-chnage matrix, genes (features) in rows and samples
in columns</dd>
<dt>reference</dt>
<dd>The reference value that should be set as 0 in the scores,
default: 0</dd>
<dt>choices</dt>
<dd>How many PCs should be retured. Passed to <code>pcaScores</code></dd>
<dt>reverse</dt>
<dd>Whether the axes should be reversed. Passed to
<code>pcaScores</code>
Perform PCA and get scores from a logFC matrix by setting a pseudo profile
of no change (0 for all features) at the origin point</dd></dl>

Arguments

Perform principal component analysis and derive PCA scores from a logFC
matrix — pcaScoresFromLogFC

<dl>

<dt>lfcMat</dt>
<dd>Log fold-chnage matrix, genes (features) in rows and samples
in columns</dd>


<dt>reference</dt>
<dd>The reference value that should be set as 0 in the scores,
default: 0</dd>


<dt>choices</dt>
<dd>How many PCs should be retured. Passed to <code>pcaScores</code></dd>


<dt>reverse</dt>
<dd>Whether the axes should be reversed. Passed to
<code>pcaScores</code>
Perform PCA and get scores from a logFC matrix by setting a pseudo profile
of no change (0 for all features) at the origin point</dd>

</dl>

pcaScoresFromLogFC: Perform principal component analysis and derive PCA scores from a logFC matrix

Description

Usage

Value

Arguments

Examples