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I am trying to perform a gene ontology analysis on my single cell seq dataset in R. However R keeps giving me the error: package ‘get_ontology’ is not available (for R version 3.6.3). I have already tried two different versions:4.0.0 and 3.6.0, but these two versions also gave this error. The main package ontologyIndex does work for the version 3.6.3. Is there another version I could try, or do people have any tips for the get_ontology function?

Fenne v
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  • `get_ontology` is not a package, it's a function in a package (`ontologyIndex`). You must install the *package* and load it with `library(ontologyIndex)` before using the *function*. Also, what have you tried? What code have you run exactly? – Rui Barradas Jun 06 '20 at 16:22
  • R is correct insofar as there is no package `get_ontology`. There is a function `get_ontology` provided by the package `ontologyIndex`. It seems you try to load the function with `library(get_ontology)` what doesn't work (because it's a function). – starja Jun 06 '20 at 16:23
  • I have run the code install.packages(get_ontology). Butnow I have read that the get_ontology is not a package but a function :) The reason I tried this was because I got this error Error in get_ontology(x, name = paste(names(df.list[i]), "Pathways for top 100 genes", : unused arguments (name = paste(names(df.list[i]), "Pathways for top 100 genes", sep = " "), return.data = T, full_GSEA = F) – Fenne v Jun 06 '20 at 17:51
  • , after I run this code: x <- data.frame(gene = rownames(df.list[[i]]), avg_logFC = 0) get_ontology(x, name = paste("Cluster", names(df.list[i]), "Pathways for top 100 genes", sep = " "), return.data = T, full_GSEA = F) – Fenne v Jun 06 '20 at 17:52

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