Package test failed

[gianfilippo]

Hi,

I should also report that the test data failed as well.

I should have mentioned that I am running R 4.2.0

Thanks

Output and error below:

library(ProjecTILs) data(query_example_seurat)

Run.ProjecTILs(query_example_seurat) [1] "Loading Default Reference Atlas..." [1] "/Seurat/ref_TILAtlas_mouse_v1.rds" [1] "Loaded Reference map ref_TILAtlas_mouse_v1" [1] "Using assay RNA for query" Pre-filtering cells with scGate... No scGate model specified: using default filter for T cells

Detected a total of 34 non-pure cells for Target (2.27% of total)

[1] "34 out of 1501 ( 2% ) non-pure cells removed. Use filter.cells=FALSE to avoid pre-filtering" Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **| [1] "Aligning query to reference map for batch-correction..." |======================================================================| 100% Computing within dataset neighborhoods Finding all pairwise anchors Finding neighborhoods Finding anchors Found 645 anchors SD on anchor distances: 0.088

Projecting corrected query onto Reference PCA space

Projecting corrected query onto Reference UMAP space Error in cellstate.predict(ref = ref, query = x, reduction = reduction, : trying to get slot "misc" from an object of a basic class ("NULL") with no slots

[gianfilippo]

Hi,

I believe this error is caused by the missing ref in the cellstate.predict function call within Run.ProjecTILs. Nothing to do with my other issue

Thanks

[mass-a]

Hello Gianfilippo,

indeed one has to explicitly provide the reference to Run.ProjecTILs; we updated the Readme to specify this. Thanks for reporting the issue.

-m