GetTableCCI

GetTableCCI,scDiffCom-method

Return (a subset) of the slot <code>cci_table_raw</code> or
 <code>cci_table_detected</code> from a scDiffCom object

Analysis tools to investigate changes in intercellular
communication from scRNA-seq data. Using a Seurat object as input,
the package infers which cell-cell interactions are present in the dataset
and how these interactions change between two conditions of interest
(e.g. young vs old). It relies on an internal database of ligand-receptor
interactions (available for human, mouse and rat) that have been gathered
from several published studies. Detection and differential analyses
rely on permutation tests. The package also contains several tools
to perform over-representation analysis and visualize the results. See
Lagger, C. et al. (2023) <doi:10.1038/s43587-023-00514-x> for a full
description of the methodology.

Cyril Lagger

scDiffCom

Differential Analysis of Intercellular Communication from
scRNA-Seq Data

Eugen Ursu

Anais Equey

GetTableCCI function

<dl><dt>object</dt>
<dd><code>scDiffCom</code> object</dd>
<dt>type</dt>
<dd>Table to extract information from. Can be either
<code>"detected"</code> (default) or <code>"raw"</code>.</dd>
<dt>simplified</dt>
<dd>If <code>TRUE</code> (default) only the most
informative columns of the data.table are returned.</dd></dl>

Arguments

Return (a subset) of the slot cci_table_raw or
 cci_table_detected from a scDiffCom object — GetTableCCI

<dl>

<dt>object</dt>
<dd><code>scDiffCom</code> object</dd>


<dt>type</dt>
<dd>Table to extract information from. Can be either
<code>"detected"</code> (default) or <code>"raw"</code>.</dd>


<dt>simplified</dt>
<dd>If <code>TRUE</code> (default) only the most
informative columns of the data.table are returned.</dd>

</dl>

GetTableCCI: Return (a subset) of the slot `cci_table_raw` or `cci_table_detected` from a scDiffCom object

Description

Usage

Value

Arguments