Compute observation statistic for permutation framework

Usage

compute_observation(
  x,
  cluster_info,
  correlation_method,
  n_cores,
  test_genes,
  bin_type,
  bin_param,
  w_x,
  w_y,
  use_cm
)

Arguments

x: a SingleCellExperiment or SpatialExperiment or SpatialFeatureExperiment object
cluster_info: A dataframe/matrix containing the centroid coordinates and cluster label for each cell.The column names should include "x" (x coordinate), "y" (y coordinate), and "cluster" (cluster label).
correlation_method: A parameter pass to cor, indicating which correlation coefficient is to be computed. One of "pearson" (default), "kendall", or "spearman": can be abbreviated.
n_cores: A positive number specifying number of cores used for parallelizing permutation testing. Default is one core (sequential processing).
test_genes: A vector of strings giving the name of the genes you want to test correlation for.
bin_type: A string indicating which bin shape is to be used for vectorization. One of "square" (default), "rectangle", or "hexagon".
bin_param: A numeric vector indicating the size of the bin. If the bin_type is "square" or "rectangle", this will be a vector of length two giving the numbers of rectangular quadrats in the x and y directions. If the bin_type is "hexagonal", this will be a number giving the side length of hexagons. Positive numbers only.
w_x: a numeric vector of length two specifying the x coordinate limits of enclosing box.
w_y: a numeric vector of length two specifying the y coordinate limits of enclosing box.
use_cm: A boolean value that specifies whether to create spatial vectors for genes using the count matrix and cell coordinates instead of the transcript coordinates when both types of information are available. The default setting is FALSE.

Value

A named list with the following components

obs.stat: A matrix contains the observation statistic for every gene and every cluster. Each row refers to a gene, and each column refers to a cluster
gene_mt: contains the transcript count in each grid. Each row refers to a grid, and each column refers to a gene.