extract_subnetwork

The function extract a subnetwork from the co-expression network

Cluster-independent method based on topology structure of gene co-expression network for identifying feature gene sets, extracting cellular subpopulations, and elucidating intrinsic relationships among these subpopulations. Without prior cell clustering, SifiNet circumvents potential inaccuracies in clustering that may influence subsequent analyses. This method is introduced in Qi Gao, Zhicheng Ji, Liuyang Wang, Kouros Owzar, Qi-Jing Li, Cliburn Chan, Jichun Xie "SifiNet: a robust and accurate method to identify feature gene sets and annotate cells" (2024) <doi:10.1093/nar/gkae307>.

Qi Gao

SiFINeT

Single Cell Feature Identification with Network Topology

extract_subnetwork function

<dl><dt>so</dt>
<dd>a SiFINeT object</dd>
<dt>target_gene_name</dt>
<dd>the names of the target genes in the output network</dd>
<dt>target_gene_id</dt>
<dd>the indices of the target genes in the output network, not used when target_gene_name is not Null</dd>
<dt>positive</dt>
<dd>whether only positive (default) co-expressions or all co-expressions are considered in assigning edges</dd></dl>

Arguments

extract_subnetwork — extract_subnetwork

<dl>

<dt>so</dt>
<dd>a SiFINeT object</dd>


<dt>target_gene_name</dt>
<dd>the names of the target genes in the output network</dd>


<dt>target_gene_id</dt>
<dd>the indices of the target genes in the output network, not used when target_gene_name is not Null</dd>


<dt>positive</dt>
<dd>whether only positive (default) co-expressions or all co-expressions are considered in assigning edges</dd>

</dl>

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extract_subnetwork: extract_subnetwork

Description

Usage

Value

Arguments