navinlabcode / navinlabcode/CellTrek
keep raw data in celltrek object
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Description
I noticed that in the celltrek object that is created in the main celltrek function, only the @data matrix is kept. Is it possible to also transfer the @counts and @scale.data? I noticed these slots were empty in my final object (liver_celltrek_6b), but present in my original single nucleus seurat object (liver_sc_6b).
Thank you!
Kate
liver_celltrek_6b <- CellTrek::celltrek(
st_sc_int=traint_6b,
int_assay='traint',
sc_data=liver_sc_6b,
sc_assay = 'SCT',
reduction='pca',
intp=T,
intp_pnt=5000,
intp_lin=F,
nPCs=30,
ntree=1000,
dist_thresh=0.55,
top_spot=5,
spot_n=5,
repel_r=20,
repel_iter=20,
keep_model=T)$celltrek
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First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start at the main celltrek function, where the returned celltrek object is created, and inspect how its @data matrix is transferred from the input Seurat object. Compare the resulting object with the source object, including @counts and @scale.data; done means those requested slots are retained when available.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- r
- Domain
- data
- Issue type
- Feature
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100