Skip to content

Fix SCTransform umi.assay incorrect source assay labels #10330

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
YoukaiFromAccounting wants to merge 4 commits into
base: main
Choose a base branch
from
+10 −1
Open

Fix SCTransform umi.assay incorrect source assay labels #10330

Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
ec2527b
Correct assay used for every sctmodel
YoukaiFromAccounting Mar 13, 2026
aa75499
Update R/preprocessing.R
YoukaiFromAccounting Mar 13, 2026
e26c2cb
Merge branch 'main' into fix-sctransform-modelassay
YoukaiFromAccounting Mar 13, 2026
e5591bb
Merge branch 'main' into fix-sctransform-modelassay
YoukaiFromAccounting Mar 20, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
11 changes: 10 additions & 1 deletion R/preprocessing.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4288,7 +4288,16 @@ SCTransform.Seurat <- function(
verbose = verbose,
...)
assay.data <- SCTAssay(assay.data, assay.orig = assay)
slot(object = slot(object = assay.data, name = "SCTModel.list")[[1]], name = "umi.assay") <- assay

# Extract all SCT models stored in assay
sct_models <- slot(object = assay.data, name = "SCTModel.list")

# Update umi.assay field for every SCT model
for (i in seq_along(sct_models)) {
slot(object = sct_models[[i]], name = "umi.assay") <- assay
}
slot(object = assay.data, name = "SCTModel.list") <- sct_models
Comment on lines +4292 to +4299

object[[new.assay.name]] <- assay.data

if (verbose) {
Expand Down
Loading