Error with export2scope function

[Sophia409]

Hi, @cflerin @s-aibar since the question #88 hasn't been solved, I open a new issue about this question.
I do find scenic.loom file in the output folder, not sure if it is available with error reported. Or how can i try another way to export my output to a loom file?

> scenicOptions@fileNames$output["loomFile",] <- "output/N28_SCENIC.loom"
> export2scope(scenicOptions, exprMat_filtered)
The folowing cell metadata will be added:
                type
CellType      factor
nFeature_RNA integer
nCount_RNA   numeric
time_sum      factor
[1] "Adding global attributes..."
[1] "Adding matrix..."
  |========================================================================================| 100%[1] "Adding column attributes..."
[1] "Adding default metrics nGene..."
[1] "Adding default embedding..."
[1] "Adding row attributes..."
[1] "Adding columns edges..."
[1] "Adding row edges..."
[1] "Adding layers..."
Error in ds$write_low_level(robj) : 
  Robj to convert does not match enum datatype

[TatyanaLev]

I'm having an identical problem while using the provided tutorial data...

[widsquid]

here is the rest of what I used to complete the pipeline and generate a file that I was able to visualize and analyze on their website tool. Perhaps if you notice any differences here from your attempt you can try this with your data and see if it works. (see issue #88) W

SCENIC.txt

[ls3456]

This works for me.

scenicOptions@fileNames$output["loomFile",] <- "output/human.loom" fileName <- getOutName(scenicOptions, "loomFile") scenicOptions@inputDatasetInfo$cellInfo = cellInfo export2scope(scenicOptions,exprMat)

This is my cellnfo object. cellInfo <- data.frame(seuratCluster=Idents(aggre)) head(cellInfo) cellInfo <- data.frame(cellInfo) cellTypeColumn <- "seuratCluster" colnames(cellInfo)[which(colnames(cellInfo)==cellTypeColumn)] <- "CellType"