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

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Documentation for package ‘Statial’ version 1.9.0

• 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