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Error when using Sim_Wang_2007 in simplifyGOFromMultipleLists #112

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Cjy0219 opened this issue Oct 11, 2024 · 0 comments
Open

Error when using Sim_Wang_2007 in simplifyGOFromMultipleLists #112

Cjy0219 opened this issue Oct 11, 2024 · 0 comments

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@Cjy0219
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Cjy0219 commented Oct 11, 2024

Hi! Thanks for your excellent tool! Recently, I have been trying to use the simplifyGOFromMultipleLists() function of package version 1.99.0, but I get the following error message:

SimplifyGOFromMultipleLists(go_id_list,ont = "BP",measure = "Sim_Wang_2007",db = "org.Mm.eg.db")
Use column 'ID' as `go_id_column`.
Use column 'p.adjust' as `padj_column`.
1403/2739 GO IDs left for clustering.
term_sim_method: Sim_Wang_2007
**Error in (function (dag, terms, contribution_factor = c(is_a = 0.8, part_of = 0.6),  : 
  Contribution factor should be provided for all relations.**

I tried to change the contribution_factor, but it did not work.

simplifyGOFromMultipleLists(go_id_list,ont = "BP",measure = "Sim_Wang_2007",db = "org.Mm.eg.db",control=list(contribution_factor=c("is_a"=0.8,"part_of"=0.6,"regulates"=0.6,"negatively_regulates"=0.8,"positively_regulates"=0.8)))

part of my sessionInfo:[1] GOSemSim_2.28.1           simplifyEnrichment_1.99.0

Could you please help? I look forward to your reply, and thank you for your attention to this matter.

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