Differential neighbourhood abundance testing on a graph


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Documentation for package ‘miloR’ version 2.4.1

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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