interaction_variable {spatialTIME}

Bivariate Interaction Variable

Description

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

Usage

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