convertToPagoda2

Convert Conos object to Pagoda2 object

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

convertToPagoda2 function

<dl><dt>con</dt>
<dd>Conos object</dd>
<dt>n.pcs</dt>
<dd>numeric Number of principal components (default=100)</dd>
<dt>n.odgenes</dt>
<dd>numeric Number of overdispersed genes (default=2000)</dd>
<dt>verbose</dt>
<dd>boolean Whether to give verbose output (default=TRUE)</dd>
<dt>...</dt>
<dd>parameters passed to Pagoda2$new()</dd></dl>

Arguments

Convert Conos object to Pagoda2 object — convertToPagoda2

<dl>

<dt>con</dt>
<dd>Conos object</dd>


<dt>n.pcs</dt>
<dd>numeric Number of principal components (default=100)</dd>


<dt>n.odgenes</dt>
<dd>numeric Number of overdispersed genes (default=2000)</dd>


<dt>verbose</dt>
<dd>boolean Whether to give verbose output (default=TRUE)</dd>


<dt>...</dt>
<dd>parameters passed to Pagoda2$new()</dd>

</dl>

convertToPagoda2: Convert Conos object to Pagoda2 object

Description

Usage

Value

Arguments