# Spatial Interaction Markers

## Documentation for package ‘SpaceMarkers’ version 1.2.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

curated_genes | Curated Genes for example purposes
find_genes_of_interest | find_genes_of_interest Identify genes associated with pattern interaction. This function identifies genes exhibiting significantly higher values of testMat in the Interaction region of the two patterns compared to regions with exclusive influence from either pattern. It uses Kruskal-Wallis test followed by posthoc analysis using Dunn's Test to identify the genes.
getInteractingGenes | getInteractingGenes Calculate Interaction Regions and Associated Genes This function calculates statistically significant genes using a non-parametric Kruskal-Wallis test for genes in any one region of influence and a post hoc Dunn's test is used for analysis of genes between regions.
getPairwiseInteractingGenes | getPairwiseInteractingGenes
getSpatialFeatures | getSpatialFeatures Load spatial features
getSpatialParameters | getSpatialParameters Calculate the Optimal Parameters for Interacting Cells
load10XCoords | load10XCoords Load 10x Visium Spatial Coordinates
load10XExpr | load10XExpr load 10X Visium Expression Data
optParams | Optimal paramters of 5 patterns from CoGAPS.