Skip to contents

Calculate gene spatial auto-correlations

rs_hotspot_autocor.Rd

This function implements the HotSpot auto-correlation functionality and will return to what extent a given gene shows auto-correlation in the generated kNN-graph from the embeddings. For details see DeTomaso, et al.

Usage

rs_hotspot_autocor(
  f_path_genes,
  f_path_cells,
  embd,
  hotspot_params,
  cells_to_keep,
  genes_to_use,
  streaming,
  verbose,
  seed
)

Arguments

f_path_genes

Path to the counts_genes.bin file.

f_path_cells

Path to the counts_cells.bin file.

embd

Numerical matrix. The embedding matrix from which to generate the kNN graph.

hotspot_params

List. The HotSpot parameter list.

cells_to_keep

Integer vector. 0-index vector indicating which cells to include in the analysis. Ensure that this is of same order/length as the embedding matrix.

genes_to_use

Integer vector. 0-index vector indicating which genes to include.

streaming

Boolean. Shall the data be streamed in chunks. Useful for large data sets.

verbose

Boolean. Controls verbosity of the function.

seed

Integer. Random seed for reproducibility.

Value

A list with the following elements.

  • gene_idx - 0-based integer indicating the gene index.

  • gaerys_c - Gaery's C calculation for the autocorrelation coefficient.

  • z_score - Z-score of the auto-correlation.

  • pval - P-value derived from the Z-score.

  • fdr - False discovery rate based on the p-value.

References

DeTomaso, et al., Cell Systems, 2021