Man pages for MarioniLab/miloR
Differential neighbourhood abundance testing on a graph
| 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... |
| fitGLMM | Perform differential abundance testing using a NB-generalised... |
| fitPLGlmm | GLMM parameter estimation using pseudo-likelihood |
| glmmControl.defaults | glmm control default values |
| 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 |
| methods | Get and set methods for Milo objects |
| Milo | The Milo constructor |
| miloR | miloR |
| miloR-package | The miloR package |
| plotDAbeeswarm | Visualize DA results as a beeswarm plot |
| plotNhoodCounts | Plot the number of cells in a neighbourhood per sample and... |
| plotNhoodExpressionDA | 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 |
| 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 |
