Closed Jacobog02 closed 2 years ago
Since the scATAC-seq data is not normalized by SCTransform, you can't set normalization.method="SCT"
in FindTransferAnchors()
. To integrate scRNA-seq and scATAC-seq data, you will need to log-normalize the RNA expression data instead.
Computing transfer anchors between scATAC obj with gene activity scores and CITE-seq dataset with SCT normalized expression values. I expect the transferanchor object to be returned but the function errors about the reference object not having VariableFeatures computed. I have double checked the variable features of the input object are present so I believe the issue is within the function itself.
minimal reproducible code example (be warned,takes over 20min to run) This example follows the Signac tutorial for reference mapping.
Specifically the error gives
Doing some quick debugging for the function I believe this is caused by the
reference
Seurat object (near line 781 of R/integration.R ) does not capture the input reference VariableFeatures field to pass along to downstream functions. This is interesting as other scRNA-seq references w/o SCT normalization allows the RunCCA function to run.Thanks for the help!