.compute_reduction

Compute PCA or UMAP on expression data when not available in stored reductions.

internal

Investigate the evolution of biological processes by capturing evolutionary signatures in transcriptomes (Drost et al. (2018) <doi:10.1093/bioinformatics/btx835>). This package aims to provide a transcriptome analysis environment to quantify the average evolutionary age of genes contributing to a transcriptome of interest.

Hajk-Georg Drost

myTAI

Evolutionary Transcriptomics

Stefan Manolache

Jaruwatana Sodai Lotharukpong

Nikola Kalábová

Filipa Martins Costa

Kristian K Ullrich

.compute_reduction function

<dl><dt>expression</dt>
<dd>Expression matrix with genes as rows and cells as columns</dd>
<dt>method</dt>
<dd>Character string: "PCA" or "UMAP"</dd>
<dt>seed</dt>
<dd>Integer seed for reproducible results (default: 42)</dd></dl>

Arguments

Compute Dimensional Reduction — .compute_reduction

<dl>

<dt>expression</dt>
<dd>Expression matrix with genes as rows and cells as columns</dd>


<dt>method</dt>
<dd>Character string: "PCA" or "UMAP"</dd>


<dt>seed</dt>
<dd>Integer seed for reproducible results (default: 42)</dd>

</dl>

.compute_reduction: Compute Dimensional Reduction

Description

Usage

Value

Arguments