GEX_coexpression_coefficient

Returns eiter a plot or numeric data of coexpression levels of selected genes.Coexpression % is calculated as the quotient of double positive cells (counts \&gt; 0) and the sum of total cells positive for either genes.

We present 'Platypus', an open-source software platform providing a user-friendly interface to investigate B-cell receptor and T-cell receptor repertoires from scSeq experiments. 'Platypus' provides a framework to automate and ease the analysis of single-cell immune repertoires while also incorporating transcriptional information involving unsupervised clustering, gene expression and gene ontology. This R version of 'Platypus' is part of the 'ePlatypus' ecosystem for computational analysis of immunogenomics data: Yermanos et al. (2021) <doi:10.1093/nargab/lqab023>, Cotet et al. (2023) <doi:10.1093/bioinformatics/btad553>.

Alexander Yermanos

Platypus

Single-Cell Immune Repertoire and Gene Expression Analysis

Andreas Agrafiotis

Victor Kreiner

Tudor-Stefan Cotet

Raphael Kuhn

Danielle Shlesinger

Jiami Han

Vittoria Martinolli D'Arcy

Lucas Stalder

Daphne van Ginneken

GEX_coexpression_coefficient function

<dl><dt>GEX</dt>
<dd>GEX seurat object generated with VDJ_GEX_matrix (VDJ_GEX_matrix.output\[\[2\]\])</dd>
<dt>genes</dt>
<dd>Character vector. At least 2 genes present in rownames(GEX). Use "all" to include all genes. The number of comparisons to make is the length(genes)! (factorial). More than 100 genes are not recommended.</dd>
<dt>subsample.n</dt>
<dd>Interger. Number of cells to subsample. If set to 100, 100 cells will be randomly sampled for the calculation</dd>
<dt>plot.dotmap</dt>
<dd>Boolean. Whether to return a plot</dd></dl>

Arguments

Coexpression of selected genes — GEX_coexpression_coefficient

<dl>

<dt>GEX</dt>
<dd>GEX seurat object generated with VDJ_GEX_matrix (VDJ_GEX_matrix.output\[\[2\]\])</dd>


<dt>genes</dt>
<dd>Character vector. At least 2 genes present in rownames(GEX). Use "all" to include all genes. The number of comparisons to make is the length(genes)! (factorial). More than 100 genes are not recommended.</dd>


<dt>subsample.n</dt>
<dd>Interger. Number of cells to subsample. If set to 100, 100 cells will be randomly sampled for the calculation</dd>


<dt>plot.dotmap</dt>
<dd>Boolean. Whether to return a plot</dd>

</dl>

Coexpression of selected genes

GEX_coexpression_coefficient: Coexpression of selected genes

Description

Usage

Value

Arguments

Examples