Note that I have one !!TODO! little bit in there since whether we end up with suspension_type (vs just keeping it as seq_unit) depends on that https://github.com/AlexsLemonade/scpca-nf/issues/681 as well. I imagine we'll be keeping it as seq_unit since we don't need CZI compliance for merged objects?
There are also a few corrections I made along the way to SCE merged objects that I noticed:
We were missing the additional_modalities column in colData
The metadata(merged_sce)$library_metadata$SCPCL000000 list was missing a few fields, and it also incorrectly listed sample_metadata which was removed.
Fixed a couple typos, also in sce_object_contents.md where the same typo was in both files.
Also, in sce_object_contents.md, suspension_type was missing from the AnnDataobs slot, and it indeed appears to be in those objects (checked on in scpca-prod).
Towards #241 This is the first of two PRs (second coming after https://github.com/AlexsLemonade/scpca-nf/issues/681 is wrapped up) to fill in the rest of the
AnnData
docs for merged objects.Note that I have one
!!TODO!
little bit in there since whether we end up withsuspension_type
(vs just keeping it asseq_unit
) depends on that https://github.com/AlexsLemonade/scpca-nf/issues/681 as well. I imagine we'll be keeping it asseq_unit
since we don't need CZI compliance for merged objects?There are also a few corrections I made along the way to
SCE
merged objects that I noticed:additional_modalities
column incolData
metadata(merged_sce)$library_metadata$SCPCL000000
list was missing a few fields, and it also incorrectly listedsample_metadata
which was removed.sce_object_contents.md
where the same typo was in both files.sce_object_contents.md
,suspension_type
was missing from theAnnData
obs
slot, and it indeed appears to be in those objects (checked on inscpca-prod
).