Dear all,

I have a list of peaks from ChIPseq experiments. Now I am trying to find to over which genes these peaks overlap (and extract the gene name).
I'm sure this should be pretty easy, but I am just starting with bioconductor, so some concepts are still vague.
Here's what I did so far:

# Not run because it is installed (as well as other packages)
# source("http://bioconductor.org/biocLite.R")
# biocLite("TxDb.Dmelanogaster.UCSC.dm3.ensGene")
# Load the Dmelanogaster genome
library(TxDb.Dmelanogaster.UCSC.dm3.ensGene, quietly = TRUE)
txdb <- TxDb.Dmelanogaster.UCSC.dm3.ensGene
ee <- exonsBy(txdb, "gene")

# Load an subset of my peaks for the sake of the example
finalPeaks <- rbind(c("chr3R", "2788500", "2842850", "2815675", "54350"), (c("chr3R", "12484350", "12661350", "12572850", "177000")))
rownames(finalPeaks) <- c("Peak 1", "Peak 2")
colnames(finalPeaks) <- c("chr", "start", "end", "center", "length")

# Create a GRanges object with the file I have 
# finalPeaks is a matrix with rows being individual peaks and columns <- c()
GRfinalPeaks <- GRanges(finalPeaks[,1], IRanges(start = as.numeric(finalPeaks[,2]), end = as.numeric(finalPeaks[,3])))

I'm stuck from here. What I'd like is to get, for each peak, the overlapping genes.
For example, an output that would be:

Peak1: GeneA, GeneB, GeneC, etc
Peak2: GeneD

Also, I don't know how simple it is because (as specified in the output example) one peak can overlap several genes or none at all..
Thanks for any help,

Patrick
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