I try to convert sce object to seurat . it works but I'm loosing features containes in rowData/colData. How to get them in the seurat object ? What am I missing ? (https://satijalab.org/seurat/archive/v3.0/conversion_vignette.html)
> sce.to.seurat <- as.Seurat(seurat.to.sce)
class: SingleCellExperiment
dim: 33694 4570
metadata(0):
assays(2): counts logcounts
rownames(33694): RP11-34P13.3 FAM138A ... AC213203.1 FAM231B
rowData names(9): vst.mean vst.variance ... **feature_ensembl**
**feature_symbol**
colnames(4570): OSI_TIPI_Vertes_AAACCCAAGGTAAGGA-1
OSI_TIPI_Vertes_AAACCCATCGAACACT-1 ...
OSI_TIPI_Rouges_TTTGTTGGTCCAATCA-1 OSI_TIPI_Rouges_TTTGTTGGTGGTCTTA-1
colData names(12): orig.ident nCount_RNA ... detected total
reducedDimNames(0):
altExpNames(0):
>head(sce.to.seurat@meta.data))
OSI_TIPI_Vertes 36827 6424
OSI_TIPI_Vertes_AAACCCATCGAACACT-1 OSI_TIPI_Vertes 56588 7438
log10GenesPerUMI mitoRatio S.Score
OSI_TIPI_Vertes_AAACCCAAGGTAAGGA-1 0.8339174 2.51989030 -0.04258605
G2M.Score Phase ident sum
OSI_TIPI_Vertes_AAACCCAAGGTAAGGA-1 -0.09878542 G1 OSI_TIPI_Vertes 36827
detected total
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ZheFrench
1 answer
You're honestly better off recreating the Seurat object manually via CreateSeuratObject(). The as.Seurat() function doesn't transfer info well and has been mildly broken for years at this point. It doesn't even attempt to transfer rowData if I remember correctly.
Something like this is your best bet:
sce.to.seurat <- CreateSeuratObject(counts = counts(seurat.to.sce), meta.data = as.data.frame(colData(seurat.to.sce)))
sce.to.seurat <- SetAssayData(object = sce.to.seurat, slot = "data", new.data = logcounts(seurat.to.sce))
# Set feature metadata, AKA rowData. Super intuitive, right?
sce.to.seurat[["RNA"]][[]] <- as.data.frame(rowData(seurat.to.sce))
Ah. I got that bit from this issue, which is a bit old at this point. I do not know French, so I can't comment on the error. It seems like maybe they're adding support for this soon at least.
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