# Differential neighbourhood abundance testing on a graph

## Documentation for package ‘miloR’ version 2.2.0

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

## Help Pages

miloR-package | The miloR package
annotateNhoods | Add annotations from colData to DA testing results
buildFromAdjacency | Build a graph from an input adjacency matrix
buildGraph | Build a k-nearest neighbour graph
buildNhoodGraph | Build an abstracted graph of neighbourhoods for visualization
calcNhoodDistance | Calculate within neighbourhood distances
calcNhoodExpression | Average expression within neighbourhoods
checkSeparation | Check for separation of count distributions by variables
computePvalue | Compute the p-value for the fixed effect parameters
countCells | Count cells in neighbourhoods
findNhoodGroupMarkers | Identify post-hoc neighbourhood marker genes
findNhoodMarkers | Identify post-hoc neighbourhood marker genes
fitGeneticPLGlmm | GLMM parameter estimation using pseudo-likelihood with a custom covariance matrix
fitGLMM | Perform differential abundance testing using a NB-generalised linear mixed model
fitPLGlmm | GLMM parameter estimation using pseudo-likelihood
glmmControl.defaults | glmm control default values
graph | Get and set methods for Milo objects
graph-method | Get and set methods for Milo objects
graph<- | Get and set methods for Milo objects
graph<--method | Get and set methods for Milo objects
graphSpatialFDR | Control the spatial FDR
groupNhoods | Group neighbourhoods
initialiseG | Construct the initial G matrix
initializeFullZ | Construct the full Z matrix
makeNhoods | Define neighbourhoods on a graph (fast)
matrix.trace | Compute the trace of a matrix
Milo | The Milo constructor
Milo-class | The Milo constructor
Milo-methods | Get and set methods for Milo objects
miloR | miloR
nhoodAdjacency | Get and set methods for Milo objects
nhoodAdjacency-method | Get and set methods for Milo objects
nhoodAdjacency<- | Get and set methods for Milo objects
nhoodAdjacency<--method | Get and set methods for Milo objects
nhoodCounts | Get and set methods for Milo objects
nhoodCounts-method | Get and set methods for Milo objects
nhoodCounts<- | Get and set methods for Milo objects
nhoodCounts<--method | Get and set methods for Milo objects
nhoodDistances | Get and set methods for Milo objects
nhoodDistances-method | Get and set methods for Milo objects
nhoodDistances<- | Get and set methods for Milo objects
nhoodDistances<--method | Get and set methods for Milo objects
nhoodExpression | Get and set methods for Milo objects
nhoodExpression-method | Get and set methods for Milo objects
nhoodExpression<- | Get and set methods for Milo objects
nhoodExpression<--method | Get and set methods for Milo objects
nhoodGraph | Get and set methods for Milo objects
nhoodGraph-method | Get and set methods for Milo objects
nhoodGraph<- | Get and set methods for Milo objects
nhoodGraph<--method | Get and set methods for Milo objects
nhoodIndex | Get and set methods for Milo objects
nhoodIndex-method | Get and set methods for Milo objects
nhoodIndex<- | Get and set methods for Milo objects
nhoodIndex<--method | Get and set methods for Milo objects
nhoodReducedDim | Get and set methods for Milo objects
nhoodReducedDim-method | Get and set methods for Milo objects
nhoodReducedDim<- | Get and set methods for Milo objects
nhoodReducedDim<--method | Get and set methods for Milo objects
nhoods | Get and set methods for Milo objects
nhoods-method | Get and set methods for Milo objects
nhoods<- | Get and set methods for Milo objects
nhoods<--method | Get and set methods for Milo objects
plotDAbeeswarm | Visualize DA results as a beeswarm plot
plotNhoodCounts | Plot the number of cells in a neighbourhood per sample and condition
plotNhoodExpressionDA | Visualize gene expression in neighbourhoods
plotNhoodExpressionGroups | Visualize gene expression in neighbourhoods
plotNhoodGraph | Plot graph of neighbourhood
plotNhoodGraphDA | Plot Milo results on graph of neighbourhood
plotNhoodGroups | Plot graph of neighbourhoods coloring by nhoodGroups
plotNhoodMA | Visualize DA results as an MAplot
plotNhoodSizeHist | Plot histogram of neighbourhood sizes
Satterthwaite_df | Compute degrees of freedom using Satterthwaite method
show | Get and set methods for Milo objects
show-method | Get and set methods for Milo objects
sim_discrete | sim_discrete
sim_family | sim_family
sim_nbglmm | sim_nbglmm
sim_trajectory | Simulated linear trajectory data
testDiffExp | Perform post-hoc differential gene expression analysis
testNhoods | Perform differential neighbourhood abundance testing