Best way to store VDJ data in object

[rnabioco]

Best way to store VDJ data in object

[kriemo]

For storing verbose per cell or per clonotype meta.data we could include it in the @misc slot, which is just a list. We could then write methods around accessing and manipulating the data as needed.

i.e.
seurat_object@misc$VDJ
seurat_object@misc$VDJ$BCR_clustering
seurat_object@misc$CDJ$Lineage_trees
etc.

[sheridar]

I think this is a good idea, then we don't have to worry about downstream issues with different Seurat functions.
We could still include VDJ info in the meta.data, which would have NAs. The only issue I've encountered so far with this is you can't assign cell Idents() using a meta.column with NAs.

[sheridar]

Code that adds a separate VDJ assay
https://github.com/rnabioco/Rincon_scVDJseq/blob/7e5742dfc4f168dcc909b91e3f9355ae9f397c3c/results/qc.Rmd#L864