Creates network alignments using network constructed from subpopulations after PAC

Implements partition-assisted clustering and multiple alignments of networks. It 1) utilizes partition-assisted clustering to find robust and accurate clusters and 2) discovers coherent relationships of clusters across multiple samples. It is particularly useful for analyzing single-cell data set. Please see Li et al. (2017) <doi:10.1371/journal.pcbi.1005875> for detail method description.

Ye Li

Partition-Assisted Clustering and Multiple Alignments of
Networks

Dangna Li

MAN function

<dl><dt>sampleIDs</dt>
<dd>sampleID vector</dd>
<dt>num_PACSupop</dt>
<dd>number of subpopulations learned in PAC step for each sample</dd>
<dt>smallSubpopCutoff</dt>
<dd>Population size cutoff for subpopulations in clade calculation. The small subpopulations will be considered in the refinement step.</dd>
<dt>k_clades</dt>
<dd>number of clades to output before refinement</dd></dl>

Arguments

Creates network alignments using network constructed from subpopulations after PAC — MAN

<dl>

<dt>sampleIDs</dt>
<dd>sampleID vector</dd>


<dt>num_PACSupop</dt>
<dd>number of subpopulations learned in PAC step for each sample</dd>


<dt>smallSubpopCutoff</dt>
<dd>Population size cutoff for subpopulations in clade calculation. The small subpopulations will be considered in the refinement step.</dd>


<dt>k_clades</dt>
<dd>number of clades to output before refinement</dd>

</dl>

MAN: Creates network alignments using network constructed from subpopulations after PAC

Description

Usage

Value

Arguments