AnnData to Seurat: Add functionality to store X in data and raw.X in counts

[pablo-gar]

sceasy::convertFormat(h5ad_path, from="anndata", to="seurat", outFile =seurat_path, main_layer = "data")

If there was a raw layer in the source AnnData, the command above would not transfer that to the output seurat object (when main_layer=data)

Now, when executing that command:

• The matrix in the main layer of the AnnData is stored in seurat@assays$RNA@data
• And the matrix in the raw layer is stored in seurat@assays$RNA@counts

[pablo-gar]

@nh3 just bringing visibility to this

[nh3]

Many thanks @pablo-gar for the PR!

Yes, this is useful for cases where X and raw.X have the same number of genes, but what if the two slots have different number of genes?

[pablo-gar]

@nh3 do you think a sensible solution would be to resize the X and raw.X matrices to have the same number of genes?