Integrated scATAC data, dimension set: dims = 2:30

[YuelinYao]

Hi Team,

Thanks for your tool! I have a small question regarding to the scATAC integration: why do we use the dimension from 2:30 instead of 1:30 for the RunUMAP/FindIntegrationAnchors steps. Could you please kindly advise me why are we giving up the first dimension?

Many thanks,
YY

Source:
https://stuartlab.org/signac/articles/integrate_atac
-pbmc.combined <- RunUMAP(pbmc.combined, reduction = "lsi", dims = 2:30)
-integrated <- RunUMAP(integrated, reduction = "integrated_lsi", dims = 2:30)

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