Dear Christopher,

For the dataset you sent to me, you could use read.table in R and then use the 5th column (x[,5]) to parse the EnsemblID with substr or strsplit (https://stat.ethz.ch/pipermail/r-help/2008-October/178335.html).

If you follow the following steps to obtain annotated overlapping peaks, you will have a RangedData to be directly plugged into getEnrichedGO function at step 3.


 1.  Apply findOverlappingPeaks to find overlapping peaks
 2.  Apply annotatePeakInBatch to annotate the overlapping peaks
 3.  Apply getEnrichedGO to the annotated peaks from step 2.

For detailed information, please refer to http://bioconductor.org/packages/2.6/bioc/vignettes/ChIPpeakAnno/inst/doc/ChIPpeakAnno.pdf and http://bioconductor.org/packages/2.6/bioc/vignettes/ChIPpeakAnno/inst/doc/ChIPpeakAnno.pdf

Best regards,

Julie


On 2/16/11 12:29 PM, "Christopher Ricupero" <ricupero@eden.rutgers.edu> wrote:

Dear Julie,

I have a quick question that I think will be very easy for you to answer. I have been making great progress using ChIPPeak Anno and the overlapping functions.

Through this process I have generated many Overlapping and Unique Peak datasets.

However as you can see in the attached excel file example, I have unique peaks that do contain the Ensemble IDs needed for Go Annotation, but they are not contained separately. Through my comparison, the names contain the EnsemblID within the peak IDs (Ex ЦУ Conrol K9 Dy1-chr1_peak12171 ENSRNOG00000030145-Conrol K9 Dy3-chr1_peak22483 ENSRNOG00000030145Ф

However, before I run the go annotation, I will need to parse out the Ensemble ID. I can do this using the right function in Excel С=RIGHT(E2,18)Т, since all Ensemble Ids are 18 characters.

However, I would rather just complete this in R, by accessing the ranged data file and the column names that contains the Ensembl ID.

Can you tip me off on how I can just access the СnamesТ column and then just parse out the EnsemblID?

I need this so I can then run the function: getEnrichedGo.

Thank you

Christopher Ricupero
Rutgers University




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