Question: GO analysis code snippet
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gravatar for Simon Lin
12.3 years ago by
Simon Lin270
Simon Lin270 wrote:
Hello, I am looking for some GO analysis code-snippet for the following task, 1) list all the GO terms under "molecular function" 2) For a given GO id, list the associated Entrez gene IDs (or Affymetrix probe IDs for U133A) A further question: is there a package analyzeing GO hierarchically? I mean, testing the parent nodes first; if it is not significant, then, testing the children? I think most of the packages just test all the GO terms simutanuously. Thanks! Simon
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ADD COMMENTlink modified 12.3 years ago by Seth Falcon7.4k • written 12.3 years ago by Simon Lin270
Answer: GO analysis code snippet
0
gravatar for Seth Falcon
12.3 years ago by
Seth Falcon7.4k
Seth Falcon7.4k wrote:
"Simon Lin" <simonlin at="" duke.edu=""> writes: > Hello, > > I am looking for some GO analysis code-snippet for the following task, > > 1) list all the GO terms under "molecular function" You can do this at the GO level, as Jan suggested, but here's a way based on the hgu133a annotation data which makes sense given your second question... library("annotate") library("hgu133a") library("GO") isMF = filterGOByOntology(ls(hgu133aGO2ALLPROBES), "MF") mfGO = ls(hgu133aGO2ALLPROBES)[isMF] > 2) For a given GO id, list the associated Entrez gene IDs (or Affymetrix > probe IDs for U133A) At present, this takes two steps using the annotation data packages. It will get easier soon when the DB-based annotation packages are introduced. But for now... ## map a GO ID to probeset IDs hgu133aGO2ALLPROBES[[mfGO[12]]][1:5] TAS NAS NAS NAS TAS "203072_at" "203215_s_at" "203216_s_at" "204527_at" "204631_at" ## turn those into Entrez Gene IDs psids = hgu133aGO2ALLPROBES[[mfGO[12]]][1:5] unlist(mget(psids, hgu133aENTREZID)) 203072_at 203215_s_at 203216_s_at 204527_at 204631_at 4643 4646 4646 4644 4620 > A further question: is there a package analyzeing GO hierarchically? I mean, > testing the parent nodes first; if it is not significant, then, testing the > children? I think most of the packages just test all the GO terms > simutanuously. Have a look also at the GOstats package and the hyperGTest method. There are details in the vignette of how to run a conditional analysis that orders the computation bottom up (the concept is quite similar to that provided by Adrian's topGO package). You may find that the result object returned by hyperGTest in the case of GO helps you avoid the annotation data package gyrations as it gives you access to the resulting GO -> Entrez map, etc. See the vignette for details. Best, + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center BioC: http://bioconductor.org/ Blog: http://userprimary.net/user/
ADD COMMENTlink written 12.3 years ago by Seth Falcon7.4k
Answer: GO analysis code snippet
0
gravatar for Oosting, J. PATH
12.3 years ago by
Oosting, J. PATH550 wrote:
> > I am looking for some GO analysis code-snippet for the following task, > > 1) list all the GO terms under "molecular function" You could use the GOMFOFFSPRING environment from the GO package. See the example in the help. > 2) For a given GO id, list the associated Entrez gene IDs (or Affymetrix > probe IDs for U133A) The metadata packages generally do this. For EntrezGene id mapping you can use the humanLLMappings package, for the Affymetrix U133A the hgu133a2 package. > A further question: is there a package analyzeing GO hierarchically? I > mean, > testing the parent nodes first; if it is not significant, then, testing > the > children? I think most of the packages just test all the GO terms > simutanuously. The globaltest package has functionality to use the structure of the GO-graph to limit the number of tests. You should take a look at chapter 4 of the vignette for an example. Jan
ADD COMMENTlink written 12.3 years ago by Oosting, J. PATH550
Answer: GO analysis code snippet
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gravatar for Adrian Alexa
12.3 years ago by
Adrian Alexa400
Adrian Alexa400 wrote:
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ADD COMMENTlink written 12.3 years ago by Adrian Alexa400
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