Compute permutation statistics for permutation framework
Source:R/compute_permp.R
compute_permutation.RdCompute permutation statistics for permutation framework
Usage
compute_permutation(
cluster_info,
perm.size = 1000,
correlation_method = "pearson",
bin_type,
bin_param,
n.cores = 1,
w_x,
w_y,
gene_mt,
cluster_names
)Arguments
- 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).
- perm.size
A positive number specifying permutation times
- 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.- 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_typeis "square" or "rectangle", this will be a vector of length two giving the numbers of rectangular quadrats in the x and y directions. If thebin_typeis "hexagonal", this will be a number giving the side length of hexagons. Positive numbers only.- n.cores
A positive number specifying number of cores used for parallelizing permutation testing. Default is one core (sequential processing).
- 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.
- gene_mt
A matrix contains the transcript count in each grid. Each row refers to a grid, and each column refers to a gene.
- cluster_names
A list of strings giving the name and order of the clusters