| 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. |
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