Comments (4)
Hi @mkutmon, which function are you trying to use? Could you provide a quick reproducible example?
from orthogene.
I have a list of human Ensembl identifiers and would like to get the mouse Ensembl identifiers back.
mapped.data <- orthogene::convert_orthologs(gene_df = human.ids,
gene_input = "GeneID",
gene_output = "columns",
input_species = "human",
output_species = "mouse",
non121_strategy = "kbs",
method = method)
Currently, this method results in a new column "ortholog_gene" which is the mouse gene name. I would like to have the Ensembl identifier for mouse (ENSMUSG...). Is that possible?
from orthogene.
I can try and infer your use case from the above code snippet, but I'm afraid the above is not a reproducible example (i.e. i can copy and paste the code into R and it will reproduce the problem). You can read about how to make a reprex here. For future bug reports I've added an Issues template to guide users. I've attached the template for you to use here as well.
bugs_template.txt
from orthogene.
Here's an example of a reprex that i think approximates your use case:
human_genes <- orthogene::all_genes(species = "human")
method <- "gprofiler2"
mapped.data <- orthogene::convert_orthologs(gene_df = human_genes$target[1:10],
standardise_genes = TRUE,
gene_output = "columns",
input_species = "human",
output_species = "mouse",
non121_strategy = "kbs",
method = method)
mouse_genes <- orthogene::map_genes(genes = mapped.data$ortholog_gene,
species = "mouse")
Note standardise_genes = TRUE
. This means that your input ensembl IDs will be translated to human gene symbols first. These can then be translated to mouse gene symbols.
From the docs:
That said, I think a nice feature would be to do this all in one step, and return convert_orthologs
as whatever gene format is requested (not just gene symbols). I'll look into adding this feature to the next release of orthogene
.
from orthogene.
Related Issues (20)
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- babelgene tests HOT 1
- Add earthworm orthologs HOT 1
- `Matrix.utils` deprecated HOT 1
- Dependency "Matrix.utils" is no longer available HOT 2
- `rphylopic` failing HOT 3
- Replace `ggtree`/`ggimage` HOT 1
- Figure out why "Canis lupus familiaris" 1:1 orthologs are reduced HOT 3
- GHA: `Package suggested but not available: ‘rworkflows’` HOT 1
- GHA: Docker: Error: both username and password must be set to login both username and password must be set to login HOT 2
- Consider adding ortholog mappings from Zoonomia
- convert_orthologs() output is list, with "Warning: Coercing LHS to a list" HOT 5
- Consider integrating `taxize`
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from orthogene.