Bivariate Interaction Variable — interaction

Single-cell spatial-protein metric introduce by Steinhart et al in https://doi.org/10.1158/1541-7786.mcr-21-0411

interaction_variable(
  mif,
  mnames,
  r_range = NULL,
  num_permutations = 100,
  keep_permutation_distribution = FALSE,
  workers = 1,
  overwrite = FALSE,
  xloc = NULL,
  yloc = NULL
)

Arguments

mif: object of class `mif`
mnames: a character vector or table with 2 columns indicating the from-to markers to assess
r_range: numeric vector of radii for which to calculate the interaction variable at
num_permutations: integer for how many permutations to use to derive the interaction estimate under CSR
keep_permutation_distribution: boolean for whether or not to keep all permutation results or average them
workers: integer for the number of CPU cores to use for permutations, markers, and spatial samples
overwrite: boolean for whether to overwrite existing interaction variable results
xloc: column name in spatial files containing the x location - if left NULL will average columns XMin and XMax
yloc: column name in spatial files containing the y location - if left NULL will average columns YMin and YMax

Value

object of class mif with the interaction variable derive slot filled