selectIntFeatures: Select common genes for multiple data batches

In PRECAST: Embedding and Clustering with Alignment for Spatial Datasets

Select common genes for multiple data batches

Description

selectIntFeatures prioritizes genes based on the number of times they were selected as HVGs/SVGs in all data baches, and chose the top genes as the input for the analysis. We broke ties by examining the ranks of the tied genes in each original dataset and taking those with the highest median rank.

Usage

  selectIntFeatures(seulist, spaFeatureList, IntFeatures=2000)

Arguments

seulist	a list consisting of Seurat objects, where each object is a SRT data batch.
spaFeatureList	an list consisting of SVGs vectors, where each vector is the top HVGs/SVGs for each SRT data batch.
IntFeatures	the number of common HVGs/SVGs genes to be chosen.

Details

Nothing

Value

Return a string vector, the selected gene list for integration in PRECAST.

Note

nothing

Author(s)

Wei Liu

References

Wei Liu, Liao, X., Luo, Z. et al, Jin Liu* (2023). Probabilistic embedding, clustering, and alignment for integrating spatial transcriptomics data with PRECAST. Nature Communications, 14, 296

See Also

None

PRECAST documentation built on May 29, 2024, 3 a.m.