I tried to convert SingleCellExperiment to Seurat Object, but it does not work, and keep return error: Error in .subset2(x, i, exact = exact) : subscript out of bounds, how to fix it?
I have a SingleCellExperiment Obejct "scp.ref", and I would like to convert it to Seurat Object, I was using the following command:
seurat.ref <- as.Seurat(x = sce.ref, counts = NULL, data = "logcounts")
As you can see in the following output, my SingleCellExperiment object contains only logcounts, there is no raw counts there, so I followed the document of seurat and put
counts = NULL, but somehow it still does not work. I'm using R.4.0.5, Seurat 4.0. How to fix the bug?
class: SingleCellExperiment dim: 20143 33392 metadata(0): assays(1): logcounts rownames(20143): 0610010F05Rik 1110034G24Rik ... XIST-intron Zfp30 rowData names(0): colnames(33392): SuHx.PH1.SCR3_TGTCGCGAGATC SuHx.PH1.SCR3_GAATTATTCCAT ... SuHx.PH2D2.SCR10_CCGTTGTACGCG SuHx.PH2D2.SCR2_TCTCCACATTCG colData names(4): celllabel condition nFeatures nCounts reducedDimNames(0): altExpNames(0):
Errors I have:
Error in .subset2(x, i, exact = exact) : subscript out of bounds
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