Function reference • Statial

All functions

Kontextual(): Evaluation of pairwise cell relationships, conditional on a 3rd population.

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

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.

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

relabelKontextual() relabel(): Cell permutation for Kontextual