How to retrieve list of KO in R?
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4.6 years ago

I used to work with KEGG.db before it got deprecated, and now i "have" to use KEGGREST, and im kinda fighting with it to get my KO as i used to do it with KEGG.db.

Following "https://www.bioconductor.org/packages/release/bioc/vignettes/KEGGREST/inst/doc/KEGGREST-vignette.html"

I have managed to more or less understand it, but i keep getting an error when i run:

library(KEGGREST); listDatabases()

c("hsa:02010", "hsa:04142", "hsa:00600", "hsa:01100", "hsa:00071", "hsa:01100", "hsa:03320", "hsa:04146", hsa:04920", "hsa:04920", "hsa:04020", "hsa:04080", "hsa:04270") 


query <- keggGet(datos$toKEGG, "ko")

"Error in .getUrl(url, .flatFileParser) : Bad Request (HTTP 400)."

¿Is there a way i can do a mappin as i used to do (and still do) with .db packages like:

datos= select(org.Hs.eg.db,
  keys = gene_list,
  columns = c('ENTREZID','SYMBOL',"PATH"), #'GENENAME',"ONTOLOGY"   ,  "ONTOLOGYALL", "GO","GOALL",
  keytype = 'SYMBOL')

Thank you in advance, and sorry for this quite "simple" question i, despise reading tutorials and going back to my notes, cant solve.

R RNA-Seq • 865 views
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