15 Integration of Seurat objects
In Natian, it is possible to integrate processed Seurat files with an option to perform SCTransform to remove batch effects. To integrate the Seurat files, ensure they are loaded in the environment. This is achieved through either using a Seurat file created in the current running session or by resuming the processing of a Seurat file (browse and load the file).
- Select the Seurat files to integrate, and click Load button.
- Give a name for the integrated Seurat file
- Choose if you wish to perform SCtransformation.
Select features to regress out in integration from the drop down menu “Optional: select cell cycle regression options”
You can also select a reference dataset to perform reciprocal PCA based integration using the “Optional: select a reference dataset”
Reciprocal PCA based integration could be useful for large dataset integration.
Once, the input are selected, integration will commence. Note: Integration could take anywhere from several minutes to couple of hours to compelete
After the integration is completed, Natian will perform a default PCA, dimensionality reduction and clustering steps using a predefined set of parameters.
Users can repeat dimensionality reduction and clustering using resume processing the Seurat object, and using the Repeat Dimensionality reduction button.
Note SCtransform requires additional computational steps that can be memory intensive. This could result in the failure of the process if the required memory exceeds the one available on your system.
However, SCtransform is better at rectifying batch effects and clustering cells together based on biological differences.