Comments (2)
calcNhoodDistance has been superseded - the function is not deprecated for backwards compatibility. Users should use refinement_scheme="graph"
in makeNhoods
and fdr.weighting="graph-only"
in testNhoods
.
from milor.
The vignette for version 2 still illustrates calcNhoodDistance
. Can you please update the best practices to match the software? Also, did you intend to write graph-overlap
rather than graph-only
? It does not appear to be a valid parameter value.
Error in graphSpatialFDR(x.nhoods = nhoods(x), graph = graph(x), weighting = fdr.weighting, :
Weighting option not recognised - must be either k-distance, neighbour-distance, max or graph-overlap
from milor.
Related Issues (20)
- Cell Condition Relabelling Functionality HOT 3
- Prevention of Neighbourhood Merging of Similar Cell Types into Neighbourhood Groups HOT 1
- Cell type is lost during annotateNhoods HOT 5
- Function Not Found Error HOT 3
- nhood size distribution: some neighbourhoods have over 2000 cells HOT 4
- Progress Bar for GLMM HOT 6
- object 'as.SimpleList' of mode 'function' was not found when running calcNhoodDistance HOT 2
- Multiple comparisons gives identical results by using model.contrasts HOT 12
- Does MiloR take into account that the two compared conditions have different number of cells? HOT 2
- Log10 FC or Log2 FC? HOT 1
- How to use MiloR after subsetting the cell types from total cell types? HOT 4
- Direction of test for logFC calculation HOT 1
- Existence of 2 tuitorials for the "Differential abundance testing with Milo - Mouse gastrulation example" HOT 3
- Import precomputed graph HOT 7
- makeNhoods graph refinement (issue with isolated vertices) HOT 4
- No Significant Neighbourhoods Result is Error HOT 1
- Mass cytometry data HOT 1
- MiloR in spatial transcriptomics data HOT 1
- Gene expression testing of only DA neighborhoods within group?? HOT 3
- Can you implement a complete miloR in python ? HOT 1
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