stableTreeClusters

Determine number of detectable clusters given a reference walktrap and a bunch of permuted walktraps

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

stableTreeClusters function

<dl><dt>refwt</dt>
<dd>reference walktrap result</dd>
<dt>tests</dt>
<dd>a list of permuted walktrap results</dd>
<dt>min.threshold</dt>
<dd>numeric Min detectability threshold (default=0.8)</dd>
<dt>min.size</dt>
<dd>numeric Minimum cluster size (number of leafs) (default=10)</dd>
<dt>n.cores</dt>
<dd>numeric Number of cores (default=30)</dd>
<dt>average.thresholds</dt>
<dd>boolean Report a single number of detectable clusters for averaged detected thresholds (default=FALSE) (a list of detected clusters for each element of the tests list is returned by default)</dd></dl>

Arguments

Determine number of detectable clusters given a reference walktrap and a bunch of permuted walktraps — stableTreeClusters

<dl>

<dt>refwt</dt>
<dd>reference walktrap result</dd>


<dt>tests</dt>
<dd>a list of permuted walktrap results</dd>


<dt>min.threshold</dt>
<dd>numeric Min detectability threshold (default=0.8)</dd>


<dt>min.size</dt>
<dd>numeric Minimum cluster size (number of leafs) (default=10)</dd>


<dt>n.cores</dt>
<dd>numeric Number of cores (default=30)</dd>


<dt>average.thresholds</dt>
<dd>boolean Report a single number of detectable clusters for averaged detected thresholds (default=FALSE) (a list of detected clusters for each element of the tests list is returned by default)</dd>

</dl>

stableTreeClusters: Determine number of detectable clusters given a reference walktrap and a bunch of permuted walktraps

Description

Usage

Value

Arguments