R package (compatible with SCope) to create generic .loom files and extend them with other data e.g.: SCENIC regulons, Seurat clusters and markers, ...
Hello, I've been running SCENIC in R successfully but running into problems with exporting the results in loom format, which is the format utilized in the tutorials for downstream analyses of the SCENIC results. Specifically, I'm hitting the hard threshold of 245 unique values in column attributes, but I'm unable to figure out exactly what that means, or how to reduce those column attributes, or how to export the data in a different manner.
export2loom(scenicOptions, exprMat)
The folowing cell metadata will be added:
type
orig.ident character
nCount_RNA numeric
nFeature_RNA integer
Analysis character
Library character
GexCellLong character
percent.mito numeric
S.Score numeric
G2M.Score numeric
Phase character
old.ident character
nCount_SCT numeric
nFeature_SCT integer
SCT_snn_res.0.8 factor
seurat_clusters factor
Samp character
Px character
SampNum character
[1] "Adding global attributes..."
[1] "Adding matrix..."
|======================================================================| 100%[1] "Adding column attributes..."
[1] "Adding default metrics nUMI..."
[1] "Adding default metrics nGene..."
[1] "Adding default embedding..."
[1] "Adding row attributes..."
[1] "Adding columns graphs..."
[1] "Adding row graphs..."
[1] "Adding layers..."
Error in add_col_attr(loom = loom, key = cn, value = cellInfo[, cn], as.annotation = isAnnotation, :
Cannot add column attribute as an annotation with more than 245 unique values.
Hello, I've been running SCENIC in R successfully but running into problems with exporting the results in loom format, which is the format utilized in the tutorials for downstream analyses of the SCENIC results. Specifically, I'm hitting the hard threshold of 245 unique values in column attributes, but I'm unable to figure out exactly what that means, or how to reduce those column attributes, or how to export the data in a different manner.