PRECAST

An efficient data integration method is provided for multiple spatial transcriptomics data with non-cluster-relevant effects such as the complex batch effects. It unifies spatial factor analysis simultaneously with spatial clustering and embedding alignment, requiring only partially shared cell/domain clusters across datasets. More details can be referred to Wei Liu, et al. (2023) <doi:10.1038/s41467-023-35947-w>.

Wei Liu

Embedding and Clustering with Alignment for Spatial Omics
Datasets

Yi Yang

Jin Liu

PRECAST function

<dl> <dt>PRECASTObj</dt>
<dd>an object named "PRECASTObj". The object PRECASTObj is created by CreatePRECASTObject.</dd> <dt>K</dt>
<dd>An optional integer or integer vector, specify the candidates of number of clusters. if <code>K=NULL</code>, it will be set to 4~12.</dd> <dt>q</dt>
<dd>An optional integer, specify the number of low-dimensional embeddings to extract in PRECAST.</dd></dl>

Arguments

Author

Fit a PRECAST model — PRECAST

<dl>

 <dt>PRECASTObj</dt>
<dd>an object named "PRECASTObj". The object PRECASTObj is created by CreatePRECASTObject.</dd>

 <dt>K</dt>
<dd>An optional integer or integer vector, specify the candidates of number of clusters. if <code>K=NULL</code>, it will be set to 4~12.</dd>

 <dt>q</dt>
<dd>An optional integer, specify the number of low-dimensional embeddings to extract in PRECAST.</dd>

</dl>

PRECAST: Fit a PRECAST model

Description

Usage

Value

Arguments

Author

Details

References

See Also