get_cooccurrence_stats

Calculates the number of elements common between columns of two matrices.
This function performs a simple dot product when binarize = FALSE.

Analyzes spatial transcriptomic data using cells-by-genes and cell location matrices to find gene pairs that coordinate their expression between spatially adjacent cells. It enables quantitative analysis and graphical assessment of these cross-expression patterns. See Sarwar et al. (2025) <doi:10.1101/2024.09.17.613579> and <https://github.com/gillislab/CrossExpression/> for more details.

Ameer Sarwar

CrossExpression

Cross-Expression Analysis of Spatial Transcriptomics Data

Sarah Choi

Leon French

Jesse Gillis

get_cooccurrence_stats function

<dl><dt>matrix1</dt>
<dd>The first input matrix.</dd>
<dt>matrix2</dt>
<dd>The second input matrix.</dd>
<dt>sparse</dt>
<dd>If TRUE, coerces matrices to sparse format for efficiency.</dd>
<dt>binarize</dt>
<dd>If TRUE, converts matrices to binary format to count the number of common elements.</dd></dl>

Arguments

Calculates the number of elements common between columns of two matrices.
This function performs a simple dot product when binarize = FALSE. — get_cooccurrence_stats

<dl>

<dt>matrix1</dt>
<dd>The first input matrix.</dd>


<dt>matrix2</dt>
<dd>The second input matrix.</dd>


<dt>sparse</dt>
<dd>If TRUE, coerces matrices to sparse format for efficiency.</dd>


<dt>binarize</dt>
<dd>If TRUE, converts matrices to binary format to count the number of common elements.</dd>

</dl>

get_cooccurrence_stats: Calculates the number of elements common between columns of two matrices. This function performs a simple dot product when binarize = FALSE.

Description

Usage

Value

Arguments