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BBKNN implementation in Rust

rs_bbknn.Rd

[Experimental] This function implements the BBKNN algorithm from Polański, et al.

Usage

rs_bbknn(embd, batch_labels, bbknn_params, seed, verbose)

Arguments

embd

Numerical matrix. The embedding matrix to use to generate the BBKNN parameters. Usually PCA. Rows represent cells.

batch_labels

Integer vector. These represent to which batch a given cell belongs (0-indexed!).

bbknn_params

List. Contains all of the BBKNN parameters.

seed

Integer. Seed for reproducibility purposes.

verbose

Integer. 0L - quiet; 1L - normal verbosity; 2L - detailed verbosity.

Value

A list with

  • distances - Sparse list representation of the kNN distances.

  • connectivities - Sparse list representation of the connectivities.

References

Polański, et al., Bioinformatics, 2020