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I ran into an issue while using LinkPeaks() and wanted to check if anyone has experienced something similar.
I divided my dataset into three Seurat objects based on tissue types. I ran LinkPeaks() separately on each object. Two of the three objects completed the process without any problems. However, the third object consistently gets stuck at this step:
rna_object[["peaks"]] <- peaks_object[["ATAC"]]
This object was created by subsetting cells from the same original Seurat object as the others and shares an identical peak matrix structure. I’ve tried reconstructing the peak matrix and the ChromatinAssay from scratch, and even had a colleague rerun the process in a different environment—but the issue persists.
Has anyone encountered this kind of problem before, or have suggestions on what might be causing the hang at this assignment step?
Thanks in advance for any insight!
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I ran into an issue while using LinkPeaks() and wanted to check if anyone has experienced something similar.
I divided my dataset into three Seurat objects based on tissue types. I ran LinkPeaks() separately on each object. Two of the three objects completed the process without any problems. However, the third object consistently gets stuck at this step:
rna_object[["peaks"]] <- peaks_object[["ATAC"]]
This object was created by subsetting cells from the same original Seurat object as the others and shares an identical peak matrix structure. I’ve tried reconstructing the peak matrix and the ChromatinAssay from scratch, and even had a colleague rerun the process in a different environment—but the issue persists.
Has anyone encountered this kind of problem before, or have suggestions on what might be causing the hang at this assignment step?
Thanks in advance for any insight!
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