[BioC] Extracting overlapping gene names from a list of peaks

[James W. MacDonald]

Hi Patrick,

On 8/6/2013 11:48 AM, Patrick Schorderet wrote:
> 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,

 > sapply(1:2, function(x) names(ee[ee %over% GRfinalPeaks[x,],]))
[[1]]
[1] "FBgn0260642"

[[2]]
[1] "FBgn0000014" "FBgn0003944" "FBgn0015230" "FBgn0020556" "FBgn0051498"
[6] "FBgn0063261" "FBgn0084245" "FBgn0084688" "FBgn0085056"

You can then coerce that to whatever form you like.

Best,

Jim



>
> Patrick
> 	[[alternative HTML version deleted]]
>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099