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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Choice of fdr.weighting in testNhoods #299

Open bazelep opened 9 months ago

bazelep commented 9 months ago

Hello, Is there some guidance on when to use the non-default ("k-distance") option for the fdr.weighting parameter in the testNhoods() function? In the "Making comparisons for differential abundance using contrasts" vignette, the fdr.weighting parameter for the testNhoods() function is set to "graph-overlap", but it's not clear why this is chosen. Thank you, Peter Bazeley

LinearParadox commented 9 months ago

Reading the issues, it seems like the k-distance is an older and much slower approach.

99 and #249 have some details on this, but that's my read at least. I've used both on some datasets, and haven't really observed a difference in results, except the fact that k-distance takes ~15 mins on my dataset while graph overlap was seconds.

MikeDMorgan commented 8 months ago

Hi @bazelep - the recommendation is to use graph-overlap from now on. This is described in the Milo2.0 pre-print: https://doi.org/10.1101/2023.11.08.566176