Chris,

Thanks for your kind comment!

The following code snippets should do.

FeatureIDs = annotatedPeak[!is.na(annotatedPeak$distancetoFeature) & abs(annotatedPeak$distancetoFeature<5000000),]$feature
library(org.Hs.eg.db)
EnrichedGO = GetEnrichedGO(featureIDs, orgAnn="org.Hs.eg.db", maxP=0.01, multiAdj=FALSE, minGOterm=10, multiAdjMethod="")

Best regards,

Julie

On 1/20/11 3:13 PM, "Christopher Ricupero" <ricupero@eden.rutgers.edu> wrote:

Hello Dr. Zhu,

I have recently been introduced to your ChIPpeakAnno package and think it is great.

However, I am having some difficulties when working with the RangedData dataset once it is convereted and then annotated.

I followed your manuscript and exported the annotated Peak file into excel, but I would like to do something different.

What I am trying to accomplish is to filter the annotated peak Ranged Data by either the “distancetoFeature” or “shortestDistance” variables.  I am only interested in peaks that are very close to the promoter regions and TSS so I wanted to limit these distances by approx 5000 kb.  After this , I would then run the GO analysis.

Is this possible to select on this variable to get a subset of my annotated peaks before I run the enrichedGo function?

Thank  you,

Chris

Christopher Ricupero
Graduate Fellow
Rutgers Univeristy
Piscataway, NJ 08854






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