SelectModel

SelectModel.SeqK_PRECAST_Object

SelectModel.PRECASTObj

Select best PRECAST model from candidated models with different number of clusters.

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

PRECAST

Embedding and Clustering with Alignment for Spatial Datasets

Yi Yang

Jin Liu

SelectModel function

<dl> <dt>obj</dt>
<dd>a SeqK_PRECAST_Object or PRECASTObj object after PRECAST model fitting.</dd> <dt>criteria</dt>
<dd>a string, specify the criteria used for selecting the number of clusters, supporting "MBIC", "BIC" and "AIC".</dd> <dt>pen_const</dt>
<dd>an optional positive value, the adjusted constant used in the MBIC criteria.</dd> <dt>return_para_est</dt>
<dd>an optional logical value, whether return the other paramters' estimators in PRECAST.</dd></dl>

Arguments

Author

Select best PRECAST model from candidated models — SelectModel

<dl>

 <dt>obj</dt>
<dd>a SeqK_PRECAST_Object or PRECASTObj object after PRECAST model fitting.</dd>

 <dt>criteria</dt>
<dd>a string, specify the criteria used for selecting the number of clusters, supporting "MBIC", "BIC" and "AIC".</dd>

 <dt>pen_const</dt>
<dd>an optional positive value, the adjusted constant used in the MBIC criteria.</dd>

 <dt>return_para_est</dt>
<dd>an optional logical value, whether return the other paramters' estimators in PRECAST.</dd>

</dl>

SelectModel: Select best PRECAST model from candidated models

Description

Usage

Value

Arguments

Author

Details

See Also

Examples