Use milo with continuous variable

MarioniLab / miloR

R package implementation of Milo for testing for differential abundance in KNN graphs

https://bioconductor.org/packages/release/bioc/html/miloR.html

GNU General Public License v3.0

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Use milo with continuous variable #302

Closed RunyuXia closed 4 months ago

RunyuXia commented 5 months ago

Hi! I have a dataset consisting of 19 samples with ages ranging from 8 to 95 weeks. Some time points have multiple samples while some only have one. In this case, would it be appropriate to use the testNhoods function with age as a continuous covariate? I tried running the algorithm with code

milo.res <- testNhoods(milo, design = ~Age, design.df = design_df, reduced.dim='scvi', fdr.weighting="graph-overlap")

but the code ran for a very long time (>5 hrs) and I had to kill the program.

MikeDMorgan commented 5 months ago

Hi @RunyuXia - please provide the full analysis code for your analysis, including the output of sessionInfo(). The running time suggests that you haven't run makeNhoods with the refinement_scheme="graph".