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aertslab / SCopeLoomR

R package (compatible with SCope) to create generic .loom files and extend them with other data e.g.: SCENIC regulons, Seurat clusters and markers, ...
MIT License
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adding metadata to loom files #5

Closed abhisheksinghnl closed 5 years ago

abhisheksinghnl commented 5 years ago

Hi,

I am able to generate loom files using following code:

file.name <- "example.loom"
loom <- build_loom(file.name=file.name,
                   dgem=dgem,
                   title="Fake expression dataset for examples",
                   genome="Mouse", # Just for user information, not used internally
                   default.embedding=default.tsne,
                   default.embedding.name=default.tne.name)

However, when I upload these files in SCOPE, I get empty metadata columns. How can I add, say, gene expression to this loom file.

Thank you

dweemx commented 5 years ago

You should be able to query any gene expression through the gene tab. Did you finally managed to get it work?

abhisheksinghnl commented 5 years ago

Yes, I figured it out. The script will not run without dgem. My fault :(