Differential neighbourhood abundance testing on a graph

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Documentation for package ‘miloR’ version 2.4.1

• 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