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cellgeni / sceasy

A package to help convert different single-cell data formats to each other
GNU General Public License v3.0
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error convert anndata to seurat #65

Closed Polligator closed 1 year ago

Polligator commented 1 year ago

I got an error when converting anndata to seurat:

Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function 'as.matrix': 'match' requires vector arguments

it appears it has something to do with the obsm data in anndata, each of the obsm data is an array, one dimension as far as I can tell, maybe not be able to convert to a matrix?? Please advise how to fix it.

Thanks

sailseem commented 1 year ago

adata <- sc$read_h5ad("xxx.h5ad") sceasy::convertFormat(adata, from="anndata", to="seurat", outFile='xxx.rds') I got an error like this, hope anyone can help me with this

Error in path.expand(inFile) : invalid 'path' argument

zhouzhendiao commented 11 months ago

adata <- sc$read_h5ad("xxx.h5ad") sceasy::convertFormat(adata, from="anndata", to="seurat", outFile='xxx.rds') I got an error like this, hope anyone can help me with this

Error in path.expand(inFile) : invalid 'path' argument

It require file path of adata rather than adata objet.