adj_to_edgelist

Converts a spatial adjacency matrix to an edge list data frame.
Useful for integration with graph-based methods.

internal

A unified framework for detecting spatially variable genes (SVGs)
in spatial transcriptomics data. This package integrates multiple
state-of-the-art SVG detection methods including 'MERINGUE' (Moran's I based
spatial autocorrelation), 'Giotto' binSpect (binary spatial enrichment test),
'SPARK-X' (non-parametric kernel-based test), and 'nnSVG' (nearest-neighbor
Gaussian processes). Each method is implemented with optimized performance
through vectorization, parallelization, and 'C++' acceleration where applicable.
Methods are described in Miller et al. (2021) <doi:10.1101/gr.271288.120>,
Dries et al. (2021) <doi:10.1186/s13059-021-02286-2>,
Zhu et al. (2021) <doi:10.1186/s13059-021-02404-0>, and
Weber et al. (2023) <doi:10.1038/s41467-023-39748-z>.

Zaoqu Liu

Spatially Variable Genes Detection Methods for Spatial
Transcriptomics

adj_to_edgelist function

<dl><dt>adj_matrix</dt>
<dd>Square adjacency matrix.</dd>
<dt>directed</dt>
<dd>Logical. If FALSE (default), only return unique undirected edges.</dd></dl>

Arguments

Convert Adjacency Matrix to Edge List — adj_to_edgelist

<dl>

<dt>adj_matrix</dt>
<dd>Square adjacency matrix.</dd>


<dt>directed</dt>
<dd>Logical. If FALSE (default), only return unique undirected edges.</dd>

</dl>

adj_to_edgelist: Convert Adjacency Matrix to Edge List

Description

Usage

Value

Arguments