calculate_cor_mat

This Function is used to perform cell aggregation by averaging the expression of scRNA-seq matrix and then perform correlation matrix

Performing cell type annotation based on cell markers from a unified database. The approach utilizes correlation-based approach combined with association analysis using Fisher-exact and phyper statistical tests (Upton, Graham JG. (1992) <DOI:10.2307/2982890>).

Mohamed Soudy

sccca

Single-Cell Correlation Based Cell Type Annotation

Sophie LE BARS

Enrico Glaab

calculate_cor_mat function

<dl><dt>expression_mat</dt>
<dd>Seurat object that contains the expression matrix.</dd>
<dt>condition</dt>
<dd>column name of the condition in th meta data of the Seurat object.</dd>
<dt>clusters</dt>
<dd>column name of the cluster numbers in the meta data of the Seurat object.</dd>
<dt>assay</dt>
<dd>the assay to be used default is set to RNA</dd></dl>

Arguments

Mohmed Soudy <a href="/link/Mohamed.soudy%40uni.lu?package=sccca&version=0.1.1" data-mini-rdoc="sccca::Mohamed.soudy@uni.lu">Mohamed.soudy@uni.lu</a> and Sohpie LE BARS <a href="/link/sophie.lebars%40uni.lu?package=sccca&version=0.1.1" data-mini-rdoc="sccca::sophie.lebars@uni.lu">sophie.lebars@uni.lu</a> and Enrico Glaab <a href="/link/enrico.glaab%40uni.lu?package=sccca&version=0.1.1" data-mini-rdoc="sccca::enrico.glaab@uni.lu">enrico.glaab@uni.lu</a>

Author

Performs aggregation based on cell clusters and condition. Then, it calculates correlation matrix of genes — calculate_cor_mat

<dl>

<dt>expression_mat</dt>
<dd>Seurat object that contains the expression matrix.</dd>


<dt>condition</dt>
<dd>column name of the condition in th meta data of the Seurat object.</dd>


<dt>clusters</dt>
<dd>column name of the cluster numbers in the meta data of the Seurat object.</dd>


<dt>assay</dt>
<dd>the assay to be used default is set to RNA</dd>

</dl>

Mohmed Soudy <a href='mailto:Mohamed.soudy@uni.lu'>Mohamed.soudy@uni.lu</a> and Sohpie LE BARS <a href='mailto:sophie.lebars@uni.lu'>sophie.lebars@uni.lu</a> and Enrico Glaab <a href='mailto:enrico.glaab@uni.lu'>enrico.glaab@uni.lu</a>

calculate_cor_mat: Performs aggregation based on cell clusters and condition. Then, it calculates correlation matrix of genes

Description

Usage

Value

Arguments

Author