process_clus

This Function is used to get the associated cell clusters using correlation-based approach

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

process_clus function

<dl><dt>cluster</dt>
<dd>associated cluster name.</dd>
<dt>sobj</dt>
<dd>Seurat object.</dd>
<dt>assay</dt>
<dd>assay to be used default is set to RNA.</dd>
<dt>clus</dt>
<dd>cell clusters.</dd>
<dt>markers</dt>
<dd>cell markers database.</dd>
<dt>cor_m</dt>
<dd>gene correlation matrix.</dd>
<dt>m_t</dt>
<dd>overlap threshold between cell markers and expression matrix.</dd>
<dt>c_t</dt>
<dd>correlation threshold between genes.</dd>
<dt>test</dt>
<dd>statistical test that check if overlap is significant could be "p" for phyper or "f" for fisher.</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

Gets the associated cell types using correlation-based approach — process_clus

<dl>

<dt>cluster</dt>
<dd>associated cluster name.</dd>


<dt>sobj</dt>
<dd>Seurat object.</dd>


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


<dt>clus</dt>
<dd>cell clusters.</dd>


<dt>markers</dt>
<dd>cell markers database.</dd>


<dt>cor_m</dt>
<dd>gene correlation matrix.</dd>


<dt>m_t</dt>
<dd>overlap threshold between cell markers and expression matrix.</dd>


<dt>c_t</dt>
<dd>correlation threshold between genes.</dd>


<dt>test</dt>
<dd>statistical test that check if overlap is significant could be "p" for phyper or "f" for fisher.</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>

process_clus: Gets the associated cell types using correlation-based approach

Description

Usage

Value

Arguments

Author