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CostaLab / scMEGA

scMEGA: Single-cell Multiomic Enhancer-based Gene regulAtory network inference
https://costalab.github.io/scMEGA
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error in SelectTFs or GetTrajectory #25

Open rahulnutron opened 9 months ago

rahulnutron commented 9 months ago

Dear scMEGA team,

Thank you for developing this useful package. I am working with Arabidopsis datasets - GSE173834 for the scATAC data and my own scRNA-seq data. When I integrated them, at the step of SelectTFs I got this error

Creating Trajectory Group Matrix.. Error in base::rowMeans(x, na.rm = na.rm, dims = dims, ...) : 'x' must be an array of at least two dimensions

When I try to debug, it looks like, under GetTrajectory, Matrix::rowMeans fails. However, the cell_names has multiple cell names, so this should not be a vector. I will be grateful if you could help me on that. Please let me know what details you need, I will share.

Regards, Rahul

lzj1769 commented 9 months ago

Hi,

Are you using Seurat v5? It seems that the Seurat team has changed the API to get assay data. I am still working on this issue to update scMEGA functions.

Best, Zhijian