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Generate the neighbourhoods akin to the miloR approach

rs_make_milor_nhoods.Rd

Rust version of the

Usage

rs_make_milor_nhoods(embd, knn_indices, milor_params, seed, verbose)

Arguments

embd

Numeric matrix. Represents the matrix used to generate the kNN graph and will be used to refine the neighbourhoods.

knn_indices

Integer matrix. Each row represents a given cell and the columns the neighbours. (0-indexed!)

milor_params

Named list. Contains the parameters for running the miloR approach.

seed

Integer. Seed for reproducibility.

verbose

Boolean. Controls verbosity of the function.

Value

A list with the following elements:

  • index_cell - Integer. 0-indexed positions of the cells defining the neighbourhood.

  • nhoods_i - Integer. 0-indexed positions of the cells in the neighbourhood.

  • nhoods_j - Integer. To which neighbourhood the cell belongs.

  • nhoods_x - Numeric. The x-value of the COO type matrix, i.e., defaults to 1.0.

  • nrows - Integer. Number of cells in the matrix

  • ncols - Integer. Number of refined neighbourhoods.

  • kth_distances - The k-th distances for spatial FDR calculations.