get_grid_points

A function to decide grid points in a higher-dimensional space

One key exploratory analysis step in single-cell genomics data analysis
is the prediction of features with different activity levels. For example, we want
to predict differentially expressed genes (DEGs) in single-cell RNA-seq data,
spatial DEGs in spatial transcriptomics data, or differentially accessible
regions (DARs) in single-cell ATAC-seq data. 'singleCellHaystack' predicts differentially
active features in single cell omics datasets without relying on the clustering
of cells into arbitrary clusters. 'singleCellHaystack' uses Kullback-Leibler
divergence to find features (e.g., genes, genomic regions, etc) that are active
in subsets of cells that are non-randomly positioned inside an input space (such as
1D trajectories, 2D tissue sections, multi-dimensional embeddings, etc). For
the theoretical background of 'singleCellHaystack' we refer to our original paper
Vandenbon and Diez (Nature Communications, 2020) <doi:10.1038/s41467-020-17900-3>
and our update Vandenbon and Diez (Scientific Reports, 2023) <doi:10.1038/s41598-023-38965-2>.

Alexis Vandenbon

singleCellHaystack

A Universal Differential Expression Prediction Tool for
Single-Cell and Spatial Genomics Data

Diego Diez

get_grid_points function

<dl><dt>input</dt>
<dd>A numerical matrix with higher-dimensional coordinates (columns) of points (rows)</dd>
<dt>method</dt>
<dd>The method to decide grid points. Should be "centroid" (default) or "seeding".</dd>
<dt>grid.points</dt>
<dd>The number of grid points to return. Default is 100.</dd></dl>

Arguments

A function to decide grid points in a higher-dimensional space — get_grid_points

<dl>

<dt>input</dt>
<dd>A numerical matrix with higher-dimensional coordinates (columns) of points (rows)</dd>


<dt>method</dt>
<dd>The method to decide grid points. Should be "centroid" (default) or "seeding".</dd>


<dt>grid.points</dt>
<dd>The number of grid points to return. Default is 100.</dd>

</dl>

get_grid_points: A function to decide grid points in a higher-dimensional space

Description

Usage

Value

Arguments