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chanzuckerberg / single-cell-curation

Code and documentation for the curation of cellxgene datasets
MIT License
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Document R limitations that prevent Seurat conversions #390

Closed brianraymor closed 5 months ago

brianraymor commented 1 year ago

Context

See single-cell-four.

@jahilton has noted that the Seurat encoding states:

All data submitted to the cellxgene Data Portal is automatically converted to a Seurat V4 object that can be loaded by the R package Seurat.

but there are cases where conversion must be skipped due to limitations in R. See the epic Manual Seurat conversions are no longer necessary and its child issues for details.

Curators are warned during validation:

This dataset cannot be converted to the .rds (Seurat v3) format. fill-in-the-blank nonzero elements in fill-in-the-blank-matrix-name exceed the limitations in the R dgCMatrix sparse matrix class (2147483647 nonzero elements).

This limitation must also be documented in the Discover API to explain why a RDS artifact may be unavailable for consumers to download.

metakuni commented 1 year ago

See also https://app.zenhub.com/workspaces/single-cell-5e2a191dad828d52cc78b028/issues/gh/chanzuckerberg/single-cell-data-portal/4464

brianraymor commented 5 months ago

Closing. This is not a priority.