Identify spatially variable genes within each cell cluster

Usage

ctsvg_test(
  expr,
  coord,
  sc,
  cell.filter = TRUE,
  recluRes = NULL,
  min.cells = 0.01,
  seed = 2024,
  verbose = FALSE,
  n.permute = 100
)

expr: The normalized gene expression matrix
coord: The matrix of spatial locations
sc: The named vector of cell cluster assignments
cell.filter: Whether to remove spatially isolated cells within each cell cluster (TRUE by default)
recluRes: The output from recluster
min.cells: The minimum proportion of cells within each cell cluster a gene is expressed in to be retained (0.01 by default)
seed: Random seed for permutation (2024 by default)
verbose: Whether to print the cell cluster in progress (FALSE by default)
n.permute: Number of permutation times (reassigned clusters with the highest Jaccard indices, 100 by default)

A data frame with p-values and FDRs for each gene in each cell cluster