How to get the actual names of genes in celda #386
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Hi @markddesimone, thanks for your question and sorry for the delay in getting back to you. There are a few different ways to get modules and genes. If you want the topRank function to return all genes in the module, you can just increase the You can also retrieve the modules for each gene with the
This will give you a vector containing the module for each gene (note that this will be the length of genes in the altExp object which contains filtered genes and can be accessed with Lastly, you can use the
Genes will only have a non-zero probability in the module they belong to. The |
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Also, I noticed that the gene names in your topRank output are from our example dataset. Maybe you can double check that you have run |
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Celda produces a set of top genes for each Module, e.g. I get:
However my sce rownames/rowData contains 25328 actual gene_ids:
How do I map topGenes to these names? These indices do not seem to index into my list of 25k genes as they are all small numbers.
thanks for any insight
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