Cauchy.Combination

This function combines multiple p-values using the Cauchy combination method. The method is particularly useful for combining dependent p-values and is known for being robust and powerful, especially in the context of small p-values. For details, see Liu and Xie (2020).

Biotechnology in spatial omics has advanced rapidly over the past few years, enhancing both throughput and resolution. However, existing annotation pipelines in spatial omics predominantly rely on clustering methods, lacking the flexibility to integrate extensive annotated information from single-cell RNA sequencing (scRNA-seq) due to discrepancies in spatial resolutions, species, or modalities. Here we introduce the CAESAR suite, an open-source software package that provides image-based spatial co-embedding of locations and genomic features. It uniquely transfers labels from scRNA-seq reference, enabling the annotation of spatial omics datasets across different technologies, resolutions, species, and modalities, based on the conserved relationship between signature genes and cells/locations at an appropriate level of granularity. Notably, CAESAR enriches location-level pathways, allowing for the detection of gradual biological pathway activation within spatially defined domain types. More details on the methods related to our paper currently under submission. A full reference to the paper will be provided in future versions once the paper is published.

Xiao Zhang

CAESAR.Suite

CAESAR: a Cross-Technology and Cross-Resolution Framework for
Spatial Omics Annotation

Wei Liu

Jin Liu

Cauchy.Combination function

<dl><dt>pvals</dt>
<dd>A numeric vector of p-values to be combined. The p-values should be between 0 and 1.</dd>
<dt>weight</dt>
<dd>A numeric vector of weights corresponding to the p-values. If <code>NULL</code>, equal weights are assigned to all p-values. Default is <code>NULL</code>.</dd></dl>

Arguments

Combine p-values Using the Cauchy Combination Method — Cauchy.Combination

<dl>

<dt>pvals</dt>
<dd>A numeric vector of p-values to be combined. The p-values should be between 0 and 1.</dd>


<dt>weight</dt>
<dd>A numeric vector of weights corresponding to the p-values. If <code>NULL</code>, equal weights are assigned to all p-values. Default is <code>NULL</code>.</dd>

</dl>

Cauchy.Combination: Combine p-values Using the Cauchy Combination Method

Description

Usage

Value

Arguments

References

Examples