getGlobalClusterMarkers

Deprecated; Get markers for global clusters

internal

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

getGlobalClusterMarkers function

<dl><dt>conos.obj</dt>
<dd>conos object</dd>
<dt>clustering</dt>
<dd>character Name of the clustering to use (default='multi level')</dd>
<dt>min.samples.expressing</dt>
<dd>numeric Minimum number of samples that must have the genes upregulated in the respective cluster (default=0)</dd>
<dt>min.percent.samples.expressing</dt>
<dd>numeric Minumum percent of samples that must have the gene upregulated (default=0)</dd></dl>

Arguments

Deprecated; Get markers for global clusters — getGlobalClusterMarkers

<dl>

<dt>conos.obj</dt>
<dd>conos object</dd>


<dt>clustering</dt>
<dd>character Name of the clustering to use (default='multi level')</dd>


<dt>min.samples.expressing</dt>
<dd>numeric Minimum number of samples that must have the genes upregulated in the respective cluster (default=0)</dd>


<dt>min.percent.samples.expressing</dt>
<dd>numeric Minumum percent of samples that must have the gene upregulated (default=0)</dd>

</dl>

getGlobalClusterMarkers: Deprecated; Get markers for global clusters

Description

Usage

Value

Arguments