pcscore

This function computes selected principal component (PC) scores
for each sample in the given count table.

Provides methods for automatic calculation of gene scores from gene count tables, including a Z-score method that requires a table of samples being scored and a count table with control samples; a geometric mean method that does not rely on control samples; and a principal component-based method that summarizes gene expression using user-selected principal components. The Z-score and geometric mean approaches are described in Kim et al. (2018) <doi:10.1089/jir.2017.0127>.

Aris Syntakas

GeneScoreR

Gene Scoring from Count Tables

pcscore function

<dl><dt>count_table</dt>
<dd>A data frame of gene count data (genes as rows, samples as columns). All columns must be numeric.</dd>
<dt>pc</dt>
<dd>Integer vector specifying which principal components to extract (default = 1). Use "all" to return all PCs.</dd>
<dt>stabilize_sign</dt>
<dd>Logical. Should the sign of each PC be stabilized? (default = FALSE)</dd></dl>

Arguments

Calculate Principal Component Scores from Count Tables — pcscore

<dl>

<dt>count_table</dt>
<dd>A data frame of gene count data (genes as rows, samples as columns). All columns must be numeric.</dd>


<dt>pc</dt>
<dd>Integer vector specifying which principal components to extract (default = 1). Use "all" to return all PCs.</dd>


<dt>stabilize_sign</dt>
<dd>Logical. Should the sign of each PC be stabilized? (default = FALSE)</dd>

</dl>

pcscore: Calculate Principal Component Scores from Count Tables

Description

Usage

Value

Arguments

Details

Examples