mutiomic analysis

[rojinsafavi]

I am following your pbmc multiomic example (the same dataset as you provided in the toturial) And after running this block

# transfer cell type labels from reference to query
transfer_anchors <- FindTransferAnchors(
  reference = reference,
  query = pbmc,
  normalization.method = "SCT",
  reference.reduction = "spca",
  dims = 1:50
)

I get this error:

Error in FindTransferAnchors(reference = reference, query = pbmc, normalization.method = "SCT", : unused argument (reference.reduction = "pca")
Traceback:

Then I removed the reference.reduction , and re-ran:

# transfer cell type labels from reference to query
transfer_anchors <- FindTransferAnchors(
  reference = reference,
  query = pbmc,
  normalization.method = "SCT",
  dims = 1:50
)

I get this error:

Error in vst.set[[x]]: subscript out of bounds
Traceback:

1. FindTransferAnchors(reference = reference, query = pbmc, normalization.method = "SCT", 
 .     dims = 1:50)
2. GetResidual(object = reference, features = features, verbose = FALSE)
3. sapply(1:length(vst.set), function(x) rownames(vst.set[[x]]$model_pars_fit))
4. lapply(X = X, FUN = FUN, ...)
5. FUN(X[[i]], ...)
6. rownames(vst.set[[x]]$model_pars_fit)

[timoast]

The Seurat v4 beta release is required: remotes::install_github("satijalab/seurat", ref = "release/4.0.0")