interaction_variable: Bivariate Interaction Variable

In spatialTIME: Spatial Analysis of Vectra Immunoflourescent Data

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

spatialTIME documentation built on June 22, 2024, 10:35 a.m.