findSubcommunities

Increase resolution for a specific set of clusters

Wires together large collections of single-cell RNA-seq datasets, which allows for both the identification of recurrent cell clusters and the propagation of information between datasets in multi-sample or atlas-scale collections. 'Conos' focuses on the uniform mapping of homologous cell types across heterogeneous sample collections. For instance, users could investigate a collection of dozens of peripheral blood samples from cancer patients combined with dozens of controls, which perhaps includes samples of a related tissue such as lymph nodes. This package interacts with data available through the 'conosPanel' package, which is available in a 'drat' repository. To access this data package, see the instructions at <https://github.com/kharchenkolab/conos>. The size of the 'conosPanel' package is approximately 12 MB.

Evan Biederstedt

conos

Clustering on Network of Samples

Viktor Petukhov

Nikolas Barkas

Peter Kharchenko

Weiliang Qiu

findSubcommunities function

<dl><dt>con</dt>
<dd>conos object</dd>
<dt>target.clusters</dt>
<dd>clusters for which the resolution should be increased</dd>
<dt>clustering</dt>
<dd>name of clustering in the conos object to use. Either 'clustering' or 'groups' must be provided (default=NULL).</dd>
<dt>groups</dt>
<dd>set of clusters to use. Ignored if 'clustering' is not NULL (default=NULL).</dd>
<dt>method</dt>
<dd>function, used to find communities (default=leiden.community).</dd>
<dt>...</dt>
<dd>additional params passed to the community function</dd></dl>

Arguments

Increase resolution for a specific set of clusters — findSubcommunities

<dl>

<dt>con</dt>
<dd>conos object</dd>


<dt>target.clusters</dt>
<dd>clusters for which the resolution should be increased</dd>


<dt>clustering</dt>
<dd>name of clustering in the conos object to use. Either 'clustering' or 'groups' must be provided (default=NULL).</dd>


<dt>groups</dt>
<dd>set of clusters to use. Ignored if 'clustering' is not NULL (default=NULL).</dd>


<dt>method</dt>
<dd>function, used to find communities (default=leiden.community).</dd>


<dt>...</dt>
<dd>additional params passed to the community function</dd>

</dl>

findSubcommunities: Increase resolution for a specific set of clusters

Description

Usage

Value

Arguments