Man pages for MikeDMorgan/miloR
Differential neighbourhood abundance testing on a graph

annotateNhoodsAdd annotations from colData to DA testing results
buildFromAdjacencyBuild a graph from an input adjacency matrix
buildGraphBuild a k-nearest neighbour graph
buildNhoodGraphBuild an abstracted graph of neighbourhoods for visualization
calcNhoodDistanceCalculate within neighbourhood distances
calcNhoodExpressionAverage expression within neighbourhoods
checkSeparationCheck for separation of count distributions by variables
computePvalueCompute the p-value for the fixed effect parameters
countCellsCount cells in neighbourhoods
findNhoodGroupMarkersIdentify post-hoc neighbourhood marker genes
findNhoodMarkersIdentify post-hoc neighbourhood marker genes
fitGeneticPLGlmmGLMM parameter estimation using pseudo-likelihood with a...
fitGLMMPerform differential abundance testing using a NB-generalised...
fitPLGlmmGLMM parameter estimation using pseudo-likelihood
glmmControl.defaultsglmm control default values
graphSpatialFDRControl the spatial FDR
groupNhoodsGroup neighbourhoods
initialiseGConstruct the initial G matrix
initializeFullZConstruct the full Z matrix
makeNhoodsDefine neighbourhoods on a graph (fast)
matrix.traceCompute the trace of a matrix
methodsGet and set methods for Milo objects
MiloThe Milo constructor
miloRmiloR
miloR-packageThe miloR package
plotDAbeeswarmVisualize DA results as a beeswarm plot
plotNhoodCountsPlot the number of cells in a neighbourhood per sample and...
plotNhoodExpressionDAVisualize gene expression in neighbourhoods
plotNhoodGraphPlot graph of neighbourhood
plotNhoodGraphDAPlot Milo results on graph of neighbourhood
plotNhoodGroupsPlot graph of neighbourhoods coloring by nhoodGroups
plotNhoodMAVisualize DA results as an MAplot
plotNhoodSizeHistPlot histogram of neighbourhood sizes
Satterthwaite_dfCompute degrees of freedom using Satterthwaite method
sim_discretesim_discrete
sim_familysim_family
sim_nbglmmsim_nbglmm
sim_trajectorySimulated linear trajectory data
testDiffExpPerform post-hoc differential gene expression analysis
testNhoodsPerform differential neighbourhood abundance testing
MikeDMorgan/miloR documentation built on Feb. 29, 2024, 6:20 p.m.