Skip to contents

Check and Subset Spatially Varying Cross Products

check_products.Rd

Computes cross-products of standardized gene expression values and optionally filters gene pairs based on spatial autocorrelation (Moran's I).

Usage

check_products(
  gene_pair_list,
  marginals,
  cov_mat,
  ncores,
  check_morani,
  p_thresh = 0.05
)

Arguments

gene_pair_list

A data frame with two columns representing pairs of genes (by name or index).

marginals

A matrix of standardized gene expression values (e.g., output from fit_marginals()).

cov_mat

A data frame containing spatial coordinates (e.g., columns x1 and x2).

ncores

Number of CPU cores to use for parallel computation.

check_morani

Logical indicating whether to filter based on Moran's I statistic.

p_thresh

P-value threshold for filtering gene pairs by Moran's I. Default is 0.05.

Value

A list with:

gene_pair_list_subset

Filtered gene pair list (if check_morani = TRUE)

product_list

List of gene-wise expression cross-products

#'

Examples

if (FALSE) { # \dontrun{
data(test_data)
# Fit standardized marginals for gene expressions
marginal_res <- fit_marginals(
  gene_list = test_data$gene_list,
  count_mat = test_data$count_mat,
  cov_mat = test_data$cov_mat,
  formula1 = "layer_annotations",
  family1 = "nb",
  DT = TRUE,
  epsilon = 1e-6,
  ncores = 2
)
# Check and subset spatially varying cross product
check_result <- check_products(
  gene_pair_list = test_data$gene_pair_list,
  marginals = marginal_res$marginal,
  cov_mat = test_data$cov_mat,
  check_morani = FALSE, ,
  ncores = 2
)
} # }