cal_conn

cal_conn
This function calculates the first 3 order connectivities for each gene
and returns the list of vectors of connectivities.

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

cal_conn function

<dl><dt>data</dt>
<dd>Input gene by gene coexpression matrix</dd>
<dt>thres</dt>
<dd>Gene pairs with coexpression exceed thres would be assigned an
edge between them in the coexpression network</dd>
<dt>m</dt>
<dd>Sample size used for the calculation of 3rd order connectivities</dd>
<dt>abso</dt>
<dd>Whether to calculate connectivities in absolute network (TRUE)
or positive network (FALSE)</dd>
<dt>niter</dt>
<dd>Number of sample used for the calculation of 3rd order
connectivities</dd></dl>

Arguments

Author

cal_conn
This function calculates the first 3 order connectivities for each gene
and returns the list of vectors of connectivities. — cal_conn

<dl>

<dt>data</dt>
<dd>Input gene by gene coexpression matrix</dd>


<dt>thres</dt>
<dd>Gene pairs with coexpression exceed thres would be assigned an
edge between them in the coexpression network</dd>


<dt>m</dt>
<dd>Sample size used for the calculation of 3rd order connectivities</dd>


<dt>abso</dt>
<dd>Whether to calculate connectivities in absolute network (TRUE)
or positive network (FALSE)</dd>


<dt>niter</dt>
<dd>Number of sample used for the calculation of 3rd order
connectivities</dd>

</dl>

cal_conn: cal_conn This function calculates the first 3 order connectivities for each gene and returns the list of vectors of connectivities.

Description

Usage

Value

Arguments

Author