# A package to identify changes in cell state relative to spatial associations

## Documentation for package ‘Statial’ version 1.12.0

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

## Help Pages

calcContamination | Calculate the level of marker contamination of each cell
calcStateChanges | First layer wrapper function to build linear models measuring state changes
distanceCalculator | Calculate pairwise distance between cell types
getAbundances | Wrapper to calculate imhomogenous K function between a cell and surrounding types on each image
getDistances | Wrapper to calculate pairwise distance between cell types by image
getMarkerMeans | Extract the average expression for all markers for each cell type in each region defined by lisaClust
getParentPhylo | Extract parent and all children from a Phylo object
isKontextual | Test whether an object is a kontextualResult
kerenKontextual | Kontextual results from kerenSCE
kerenSCE | MIBI-TOF Breast cancer intensities
kontextCurve | Evaluation of Kontextual over a range of radii.
kontextPlot | Plotting the original and kontextual L values over a range of radii.
Kontextual | Evaluation of pairwise cell relationships, conditional on a 3rd population.
makeWindow | Creates a window for a PPP object
parentCombinations | Create all combinations of cell type relationships from a list of parents
plotStateChanges | Visualise Cell-Cell Marker Relationships
prepMatrix | Convert Kontextual or state changes result to a matrix for classification
relabel | Cell permutation for Kontextual
relabelKontextual | Cell permutation for Kontextual