sctype

This Function is used to run the sctype approach with faster implementation

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

sctype function

<dl><dt>sobj</dt>
<dd>Seurat object.</dd>
<dt>assay</dt>
<dd>assay to be used default is set to RNA.</dd>
<dt>tissue</dt>
<dd>specified tissue from which the data comes.</dd>
<dt>tt</dt>
<dd>tissue type whether 'a' for all types 'n' for normal tissues only or "c" for cancer tissues.</dd>
<dt>clus</dt>
<dd>colname in the mata.data that have the cell cluster numbers.</dd>
<dt>org</dt>
<dd>organism to be used that can be 'h' for human, 'm' for mouse, and 'a' for all markers.</dd>
<dt>scaled</dt>
<dd>indicates whether the matrix is scaled (TRUE by default)</dd>
<dt>database</dt>
<dd>name of the database to be used that can be 'sctype' or 'UMD'</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

Run the sctype approach as it's implemented by Ianevski, A., Giri, A.K. and Aittokallio, T. — sctype

<dl>

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


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


<dt>tissue</dt>
<dd>specified tissue from which the data comes.</dd>


<dt>tt</dt>
<dd>tissue type whether 'a' for all types 'n' for normal tissues only or "c" for cancer tissues.</dd>


<dt>clus</dt>
<dd>colname in the mata.data that have the cell cluster numbers.</dd>


<dt>org</dt>
<dd>organism to be used that can be 'h' for human, 'm' for mouse, and 'a' for all markers.</dd>


<dt>scaled</dt>
<dd>indicates whether the matrix is scaled (TRUE by default)</dd>


<dt>database</dt>
<dd>name of the database to be used that can be 'sctype' or 'UMD'</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>

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sctype: Run the sctype approach as it's implemented by Ianevski, A., Giri, A.K. and Aittokallio, T.

Description

Usage

Value

Arguments

Author