# Spatial Interaction Markers

## Documentation for package ‘SpaceMarkers’ version 1.0.0

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

## Help Pages

cogaps_result | Latent Feature Space for each pattern
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.
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.