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Error in as(object@graphs$RNA_snn, "dgCMatrix") #25
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Hi, can you check if your Seurat object was generated with Seurat V3? Also, make sure that the SNN was actually built with FindNeighbors. Something like:
Let me know if that works! |
Hi, Thank you for you replay. |
Ah so For now, try using this walkthrough: https://yanwu2014.github.io/swne/Examples/multiple_pancreas_alignment_swne.html |
Hi, it works well with the workflow you provided. Thank you very much for your help. |
Thank you for creating this package. I tried to run it using a Seurat objet.
library(Seurat)
library(swne)
obj <- readRDS(file = "obj.rds")
clusters <- obj$seurat_clusters
genes.embed <- c("ENSMUSG00000031766", "ENSMUSG00000041644", "ENSMUSG00000001025", "ENSMUSG00000030963", "ENSMUSG00000032060", "ENSMUSG00000026726", "ENSMUSG00000027202", "ENSMUSG00000062209", "ENSMUSG00000054640", "ENSMUSG00000027070", "ENSMUSG00000041959", "ENSMUSG00000060803", "ENSMUSG00000097830")
swne.embedding <- RunSWNE(obj, k = 16, genes.embed = genes.embed)
Then I've got the following error:
Error in as(object@graphs$RNA_snn, "dgCMatrix") :
no method or default for coercing “NULL” to “dgCMatrix”
Is there anyway to solve this issue? Thank you very much!
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