Comments (2)
Thanks for using our package!
I'd first like to ask some clarifications on your issue, as the function you are running comes before the one referenced in issue #220.
Let us refer to the output from nichenet_seuratobj_aggregate()
as nichenet_output
. Do you mean that the DE genes you retrieved from nichenet_output$geneset_oi
and the top ligands from nichenet_output$top_ligands
are not specific to "condition_oi"?
If that is the case, then it's not an error, but the way the package was designed. For the gene set of interest (geneset_oi
), all DE genes between the two conditions are considered. If you would like to only include upregulated genes in the condition of interest, you may use the argument geneset="up"
in the function .
As for the ligands: by default, potential ligands are defined as genes expressed in at least 10% of the sender cell type (both conditions considered together) whose cognate receptors are also expressed in at least 10% of the receiver cell type. So this does not have any condition specificity in the function you are running. If you would like to only consider upregulated ligands in the analysis, you can follow the approach suggested here, or you can follow the prioritization approach here (which was the one referenced to in #220).
Hope this helps; feel free to reply to this issue if I misunderstood or if you have any further questions! 😄
from nichenetr.
Thanks for getting back to so quickly! Much appreciated.
I see, I must have misunderstood the first part. In fact I was only interested in the upregulated genes in the condition of interest. This is way I was a bit confused about the results.
I will try your suggestions and follow the other approaches linked.
Thank you very much!
from nichenetr.
Related Issues (20)
- missing function for circos plot visualization HOT 2
- I can't install nichenet HOT 1
- `make_line_plot` bugs
- `assign_ligands_to_celltype` bug when there are no general ligands
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- Warning message in `predict_ligand_activities`
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- Error when passing the recorrect_umi argument in get_lfc_celltype HOT 1
- Error in WhichCells.Seurat(object = object, idents = ident.2) : Cannot find the following identities in the object: Adjacent HOT 1
- Error in `Idents<-`: ! 'value' must be a factor or vector HOT 3
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- Low AUPR values in analyses HOT 2
- RankActiveLigands Error
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from nichenetr.