interaction_proportion_comparison_permutation_test: Calculate a permutation test result for nearest neighbors to...

In gusef/Iris: A package to extract spatial features based on multiplex IF images

Description

Calculate a permutation test result for nearest neighbors to say for each sample to see if the neighbor distance something seen under the null assumption

Usage

interaction_proportion_comparison_permutation_test(x, reference, phenotype_A,
  phenotype_B, permutations = 20, subset = NULL, verbose = FALSE, ...)

## S4 method for signature 'ImageSet'
interaction_proportion_comparison_permutation_test(x,
  reference, phenotype_A, phenotype_B, permutations, subset, verbose)

Arguments

x	IrisSpatialFeatures ImageSet object that has had extract nearest neighbors run
reference	Reference phenotype to compare proportions around
phenotype_A	First cell type to compare proportions of
phenotype_B	Second cell type to compare proportions of
permutations	Set to 100 by default
subset	Limit permutations to these types

Value

data.frame of markers and distances

Examples

#loading pre-read dataset
dataset <- IrisSpatialFeatures_data
interaction_permutation_test(dataset)

gusef/Iris documentation built on May 14, 2019, 2:42 p.m.