Integration of scatac-seq data with another integrated scRNA and scATAC data set

Question

[bioyas]

Hi all,

I am working on a 3 single cell data sets as follows:

1. scRNA-seq
2. scATAC-seq
3. scATAC-seq form multiomics

I have already processed the first two data sets (scRNA-seq & scATAC-seq). So these two data sets have been integrated.

I have a new attic data set and would like to integrate it with atac data of the old integrated object as my reference. I can do this only if I set the assay of old integrated object to "RNA". However, I want to use the "integrated" slot as my reference.

Here is the script that I am running:

Defaults(atac.old) <- "integrated"
DefaultAssay(atac.new) <- "RNA"

S.O.list <- list(old= atac.old, new = atac.new)
features <- SelectIntegrationFeatures(object.list = S.O.list, nfeatures = 6000)
reference_dataset <- 1
anchors <- FindIntegrationAnchors(object.list = S.O.list, 
                              anchor.features = features, reference = reference_dataset)
S.O.integrated.new <- IntegrateData(anchorset = anchors, new.assay.name = "INTE")
DefaultAssay(S.O.integrated.new) <- "INTE"
S.O.integrated <- ScaleData(object = S.O.integrated, verbose = FALSE)
S.O.integrated <- RunPCA(S.O.integrated, features = VariableFeatures(object = S.O.integrated))

However, this result in the following error.

Error in irlba(A = t(x = object), nv = npcs, ...) : max(nu, nv) must be positive In addition: Warning message: In PrepDR(object = object, features = features, verbose = verbose) : The following 6000 features requested have zero variance (running reduction without them):

Do you have any idea how I can fix this? Is there a way that we can use the integrated slot as our reference for next integration?