Seurat object with Harmony generate from PCA using specified features

[HarryShen668]

The loadings in my Seurat object's harmony information were generated from PCA using specified features, rather than PCA using variable features as the input. However, downstream analysis, including the buildReferenceFromSeurat function, uses variable genes. This causes an error when multiplying the matrices t(ref1$loadings) and exp_query_scaled_sync in mapQuery function because their dimensions do not match, which gives

Error in t(ref_obj$loadings) %*% exp_query_scaled_sync : 
  non-conformable arguments

If I need to use PCA with specified features for downstream analysis, including harmonization, how can I resolve this issue?

[HarryShen668]

close for problem solved