Derive an SNN from a kNN Graph object in Seurat

Usage

BuildSNNfromKNN(
  object,
  knn_choice = "RNA_nn",
  snn_name = paste0(knn_choice, "_snn"),
  prune_snn = 1/15
)

Arguments

object: Seurat object
knn_choice: Name of Graph slot to use for SNN calculation
snn_name: Name of Graph slot to store SNN
prune_snn: Threshold at which to prune SNN (set to 0 below this)

Value

Returns a Seurat object with the SNN Graph stored.

Details

code is adapted from @immunogenomics/singlecellmethods. Builds a shared nearest-neighbors graph from an input kNN using matrix multiplication so pretty quick.

References

code is adapted from @immunogenomics/singlecellmethods