fisher_spatial_cpp

Fast computation of contingency table and Fisher test p-value
for binary spatial enrichment.

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

fisher_spatial_cpp function

<dl><dt>bin_vec</dt>
<dd>Binary vector for one gene</dd>
<dt>from_idx</dt>
<dd>Vector of source indices for edges</dd>
<dt>to_idx</dt>
<dd>Vector of target indices for edges</dd></dl>

Arguments

Compute Fisher's Exact Test for Spatial Enrichment — fisher_spatial_cpp

<dl>

<dt>bin_vec</dt>
<dd>Binary vector for one gene</dd>


<dt>from_idx</dt>
<dd>Vector of source indices for edges</dd>


<dt>to_idx</dt>
<dd>Vector of target indices for edges</dd>

</dl>

fisher_spatial_cpp: Compute Fisher's Exact Test for Spatial Enrichment

Description

Usage

Value

Arguments