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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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Failure to convert SingleCellExperiment (trajectory analysis object) to h5ad #83

Open Yanst86 opened 6 months ago

Yanst86 commented 6 months ago

Hello,

I have a SingleCellExperiment, in which I computed Trajectory of Single-Cell RNA-seq data using Slingshot, which I want to convert to h5ad/Anndata.

I used this code:

library(reticulate) use_condaenv('r-sctools') sceasy::convertFormat(Traj_RNA, from="sce", to="anndata", outFile='D:/Python_coding/Trajectory_Analysis/Slingshot_Trajectory.h5ad')

And got this error:

Loading required package: TrajectoryUtils Error in as.vector(x) : no method for coercing this S4 class to a vector

Here is the structure of my object:

Traj_RNA class: SingleCellExperiment dim: 36601 39215 metadata(0): assays(2): counts logcounts rownames(36601): MIR1302-2HG FAM138A ... AC007325.4 AC007325.2 rowData names(0): colnames(39215): C01_AAACCCAAGCAATTCC-1 C01_AAACCCACACGTTGGC-1 ... R264_TTTGTTGCAGCGTACC-1 R264_TTTGTTGGTCCACACG-1 colData names(15): orig.ident nCount_RNA ... slingPseudotime_3 slingPseudotime_4 reducedDimNames(2): PCA UMAP mainExpName: RNA altExpNames(0):

Is the conversion of this type of object supported? If so, what is the fix to my problem?

Thanks in advance, Yan