Question: GOSim yeast
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7.5 years ago by
Guest User12k
Guest User12k wrote:
Hello, I'm trying to use GOSim with yeast but with no luck. The function "setEvidenceLevel(organism="yeast")" doesn't seem to work. Using the org.Sc.sgd.db library, I obtain a long list of GO terms for "856452" Yet, getGOInfo("856452") yields, No GO information available for these genes! Any help would be greatly appreciated. Yours, Fred Hoffman -- output of sessionInfo(): ID = "YHR055C" > > # get Entrez Gene ID > get(ID, org.Sc.sgdENTREZID) [1] "856452" > # get GO terms > get(ID, org.Sc.sgdGO) $`GO:0010273` $`GO:0010273`$GOID [1] "GO:0010273" $`GO:0010273`$Evidence [1] "IMP" $`GO:0010273`$Ontology [1] "BP" . . . >setEvidenceLevel(organism="yeast") > getGOInfo("856452") Error in getGOInfo("856452") : No GO information available for these genes! > setEvidenceLevel(organism="org.Sc.sgd.db") [1] "-> retrieving GO information for all available genes for organism 'org.Sc.sgd.db' in GO database" [1] "-> filtering GO terms according to evidence levels 'all'" > getGOInfo("856452") Error in getGOInfo("856452") : No GO information available for these genes! -- Sent via the guest posting facility at bioconductor.org.
go yeast gosim • 800 views
ADD COMMENTlink modified 2.7 years ago by solis0 • written 7.5 years ago by Guest User12k
Answer: GOSim yeast
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gravatar for Marc Carlson
7.5 years ago by
Marc Carlson7.2k
United States
Marc Carlson7.2k wrote:
Hi Fred, I can't speak to what is happening with GOSim:::getGOInfo. But if you are using the most recent version of bioconductor, then you could also do this kind of lookup like this: library(org.Sc.sgd.db) ID = "YHR055C" select(org.Sc.sgd.db, keys=ID, cols = c("GO","ENTREZID"), keytype="ORF") Marc On 05/22/2012 05:31 AM, Fred Hoffman [guest] wrote: > Hello, > > I'm trying to use GOSim with yeast but with no luck. The function > "setEvidenceLevel(organism="yeast")" doesn't seem to work. > > Using the org.Sc.sgd.db library, I obtain a long list of GO terms for "856452" > > Yet, getGOInfo("856452") yields, > > No GO information available for these genes! > > Any help would be greatly appreciated. > > Yours, > > Fred Hoffman > > -- output of sessionInfo(): > > > ID = "YHR055C" >> # get Entrez Gene ID >> get(ID, org.Sc.sgdENTREZID) > [1] "856452" > >> # get GO terms >> get(ID, org.Sc.sgdGO) > $`GO:0010273` > $`GO:0010273`$GOID > [1] "GO:0010273" > > $`GO:0010273`$Evidence > [1] "IMP" > > $`GO:0010273`$Ontology > [1] "BP" > > . > . > . >> setEvidenceLevel(organism="yeast") >> getGOInfo("856452") > Error in getGOInfo("856452") : > No GO information available for these genes! >> setEvidenceLevel(organism="org.Sc.sgd.db") > [1] "-> retrieving GO information for all available genes for organism 'org.Sc.sgd.db' in GO database" > [1] "-> filtering GO terms according to evidence levels 'all'" >> getGOInfo("856452") > Error in getGOInfo("856452") : > No GO information available for these genes! > > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD COMMENTlink written 7.5 years ago by Marc Carlson7.2k
Answer: GOSim yeast
0
gravatar for solis
2.7 years ago by
solis0
solis0 wrote:

Follow the next commands:

library(org.Sc.sgd.db)

setEvidenceLevel(evidences="all", organism=org.Sc.sgdORGANISM, gomap=org.Sc.sgdGO)

setOntology("BP", loadIC=FALSE)

calcICs(DIR="~/R/x86_64-redhat-linux-gnu-library/3.3/GOSim/data") # change DIR accordingly otherwise is save in the current directory

# Upload the ICs files

setOntology("BP", DIR="~/R/x86_64-redhat-linux-gnu-library/3.3/GOSim/data")

The gene IDs will depend on the database that you used when calling setEvidenceLevel. For the org.Sc.sgdGO, this is the systematic names. One way to know is by typing:

head(get("gomap", envir=GOSimEnv))

So to get the GO information or Gene Similarity use systematic IDs. For example:

getGOInfo(c("YHR043C"))
getGeneSim(c("HRA1", "ICR1"))

ADD COMMENTlink written 2.7 years ago by solis0
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