FindSVGs

Identifies features that have spatially variation along spots using SPARK-X.

Joint dimension reduction and spatial clustering is conducted for
Single-cell RNA sequencing and spatial transcriptomics data, and more details can be referred to
Wei Liu, Xu Liao, Yi Yang, Huazhen Lin, Joe Yeong, Xiang Zhou, Xingjie Shi and Jin Liu. (2022) <doi:10.1093/nar/gkac219>. It is not only computationally efficient and scalable to the sample size increment, but also is capable of choosing the smoothness parameter and the number of clusters as well.

Wei Liu

DR.SC

Joint Dimension Reduction and Spatial Clustering

Yi Yang

Jin Liu

FindSVGs function

<dl> <dt>seu</dt>
<dd>an object of class "Seurat".</dd> <dt>nfeatures</dt>
<dd>a positive integer, means how many spatially variable genes to be chosen. If there are less than 2000 features in seu, then all features are identified.</dd> <dt>covariates</dt>
<dd>a covariate matrix named control variable matrix whose number of rows is equal to the number of columns of seu.</dd> <dt>preHVGs</dt>
<dd>a positive integer, the number of highly variable genes selected for speeding up computation of SPARK-X in selecting spatially variable features.</dd> <dt>num_core</dt>
<dd>an optional positive integer, specify the cores used for identifying the SVGs in parallel.</dd> <dt>verbose</dt>
<dd>an optional logical value, whether output the related information.</dd></dl>

Arguments

Find spatially variable genes — FindSVGs

<dl>

 <dt>seu</dt>
<dd>an object of class "Seurat".</dd>

 <dt>nfeatures</dt>
<dd>a positive integer, means how many spatially variable genes to be chosen. If there are less than 2000 features in seu, then all features are identified.</dd>

 <dt>covariates</dt>
<dd>a covariate matrix named control variable matrix whose number of rows is equal to the number of columns of seu.</dd>

 <dt>preHVGs</dt>
<dd>a positive integer, the number of highly variable genes selected for speeding up computation of SPARK-X in selecting spatially variable features.</dd>

 <dt>num_core</dt>
<dd>an optional positive integer, specify the cores used for identifying the SVGs in parallel.</dd>

 <dt>verbose</dt>
<dd>an optional logical value, whether output the related information.</dd>

</dl>

FindSVGs: Find spatially variable genes

Description

Usage

Value

Arguments

Details

References

See Also

Examples