bug in doubletFinder code when reuse.pANN not FALSE

[jdrnevich]

I just installed DoubletFinder today (v2.0.4) and I was trying to walk through the Example codes show on the README (https://github.com/chris-mcginnis-ucsf/DoubletFinder?tab=readme-ov-file#example-code-for-real-world-applications) on my own data, and was fine until this part:

seu_kidney <- doubletFinder(seu_kidney, PCs = 1:10, pN = 0.25, pK = 0.09, nExp = nExp_poi.adj, reuse.pANN = "pANN_0.25_0.09_913", sct = FALSE)
Error in if (reuse.pANN) { : argument is not interpretable as logical

I tried debugging and the error is in the very first line of code where it expects reuse.pANN to either be TRUE/FALSE, not a character vector or FALSE:

debug: {
    if (reuse.pANN) {
        pANN.old <- [email protected][, reuse.pANN]
        classifications <- rep("Singlet", length(pANN.old))
        classifications[order(pANN.old, decreasing = TRUE)[1:nExp]] <- "Doublet"
        [email protected][, paste("DF.classifications", pN, pK, nExp, 
            sep = "_")] <- classifications
        return(seu)
    }

There are several ways to fix this but I'm not sure what approach you'd prefer so I didn't submit a pull request.

Thanks!