CODEWITHSUNDEEP
rstatisticsbioinformaticsbioconductor
Tonio
Tonio

Reputation: 1736

R statistical package: wrapping GOFrame objects

I'm trying to generate GOFrame objects to generate a gene ontology mapping in R for unsupported organisms (see http://www.bioconductor.org/packages/release/bioc/vignettes/GOstats/inst/doc/GOstatsForUnsupportedOrganisms.pdf).

However, following the instructions literally doesn't help me. Here's the code I execute (R 2.9.2 on ubuntu koala 64 bit)

library("AnnotationDbi")
library("org.Hs.eg.db")
frame = toTable(org.Hs.egGO)
goframeData = data.frame(frame$go_id, frame$Evidence, frame$gene_id)
goFrame = GOFrame(goframeData, organism = "Homo sapiens")

However, when i try to map my dataframe into a goFrame object, I get this mistake

Error: could not find function "GOFrame"

I'm pretty sure the GOFrame wrapper is in the AnnotationDBI library, so I'm puzzled. Any help is extra appreciated :-)

Upvotes: 1

Views: 286

Answers (2)

Dirk is no longer here
Dirk is no longer here

Reputation: 368439

As per the package description, the Go.db package is only suggested rather than depended upon. Hence, a simple

 library(GO.db)

seems to be what you need to do.

Upvotes: 1

Federico Giorgi
Federico Giorgi

Reputation: 10755

I think it's your R version. GOFrame wrapping is described to be supported in the bioconductor AnnotationDBI only since the latest release.

I just tried it and it works with R 2.10.0

Enjoy!

Upvotes: 2

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