Update run_singleR_db with bug fix and test suite#67
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Metadata assignment in Seurat object was failing due to vector name values being retained in `CL:****` format after relabeling from ontology to cell type. Assigning as vector "un-names" the values and allows for addition to Seurat metadata
kelly-sovacool
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Jun 11, 2026
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- R CMD Check is failing, see https://github.com/CCBR/SCOT/actions/runs/27307394266/job/80668762932?pr=67#step:6:270
- looks like the new data is too big. may need to be subsetted. Jing was working on subsetting a BRCA dataset in one of his PRs, maybe check with him and see what is progress is on that and perhaps you can use that dataset here.
- The linter is failing, see details https://github.com/CCBR/SCOT/actions/runs/27307394266/job/80668762945?pr=67
| mm_bm, | ||
| pattern = "^mt-" | ||
| ) | ||
| mm_bm <- subset( |
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which subset() function is being used? does it support using columns as variable names e.g. percent.mt? (see linting errors below)
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It's using the base::subset function, from what I can tell. Following the link from within leads to the base function
https://satijalab.org/seurat/articles/essential_commands#subset-seurat-objects
full boolean Co-authored-by: Kelly Sovacool, PhD <kelly-sovacool@users.noreply.github.com>
Co-authored-by: Kelly Sovacool, PhD <kelly-sovacool@users.noreply.github.com>
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It's smaller than the last dataset. It looks like an upstream failure for the other dataset. Let me dig into it |
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Changes
run_singleR_dbtests/testthat/helper-functions.Randtests/testthat/setup.Rpreprocess_sample.Rfetch_celldex_ref.Rto usecacheparameterIssues
Fixes #65
PR Checklist
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Strikethroughany points that are not applicable.)[ ] Update the docs if there are any API changes (roxygen2 comments, vignettes, readme, etc.).[ ] UpdateNEWS.mdwith a short description of any user-facing changes and reference the PR number. Follow the style described in https://style.tidyverse.org/news.htmldevtools::check()locally and fix all notes, warnings, and errors.R-CMD-checksucceeds on the most recent user commit.