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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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Which seuart data was converted to adata.X? #37

Open FADHLyemen opened 3 years ago

FADHLyemen commented 3 years ago

HI, I have three data in my seurat object object@assays$RNA@counts object@assays$RNA@data object@assays$RNA@scale.data

sceasy::convertFormat(object, from="seurat", to="anndata",
                       outFile='filename.h5ad')

my question is which data was converted to adata.X in my h5ad object?

Regards

maximilianh commented 3 years ago

Hi @Fadhl, thank you for this question. I don't know what sceasy does... it's interesting that there is another converter for this. Can I ask how you found the suggestion to use sceasy for this conversion, instead of our own converter?

The cell browser has its own tool, cbImportSeurat. This is what the cbImportSeurat documentation says:

-s MATRIXSLOT, --matrixSlot=MATRIXSLOT Export this slot of the matrix. Can be 'counts', 'data.scale' or 'data'. Default is counts

Hm, it looks like you're using a very different route for importing the data then the one I envisioned. Is it possible that your filename.h5ad contains a few different matrices?

On Mon, Jun 14, 2021 at 8:40 PM Fadhl @.***> wrote:

HI, I have three data in my seurat object @.**@. @.**@. @.**@.

sceasy::convertFormat(object, from="seurat", to="anndata", outFile='filename.h5ad')

my question is which data was converted to adata.X in my h5ad object?

Regards

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FADHLyemen commented 3 years ago

Thank you @maximilianh cellxgene VIP reccomend it and I found it more helpful than seruratdisk tool. Which link to use your tool? cbImportSeurat

maximilianh commented 3 years ago

Interesting. Sorry who is cellxgene VIP ? Did they point you towards the cell browser ? What is seuratdisk ?

You can find out cbImportSeurat as part of the cellbrowser Python package.

On Tue 15 Jun 2021 at 19:16, Fadhl @.***> wrote:

Thank you @maximilianh https://github.com/maximilianh cellxgene VIP reccomend it and I found it more helpful than seruratdisk tool. Which link to use your tool? cbImportSeurat

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FADHLyemen commented 3 years ago

I think it is data.

seurat2anndata= function(   obj, outFile = NULL, assay = 'RNA', main_layer = 'data', transfer_layers = NULL, drop_single_values = TRUE) {    

main_layer = match.arg(main_layer, c('data', 'counts', 'scale.data'))
maximilianh commented 3 years ago

@FADHLyemen Oh boy, I'm super sorry, I got the repo wrong! I thought this was the https://github.com/maximilianh/cellBrowser/ repo. I hope someone from the sceasy team will reply!