Entering edit mode
Ron,
Thanks for the positive feedback!
The function findOverlappingPeaks output additional two RangedData
sets, Peaks1withOverlaps and Peaks2withOverlaps. You can use the
following code snippet to obtain the peaks from peaks1 that do not
overlap with those from peaks2 and vice versa.
peaks1 = RangedData(IRanges(start=c(1543200,1557200,1563000,1569800,16
7889600,300),end=c(1555199,1560599,1565199,1573799,167893599,500),name
s=c("p1","p2","p3","p4","p5","p6")),strand=as.character("+"),space=c(6
,6,6,6,5,7))
peaks2 = RangedData(IRanges(start=c(1549800,1554400,1565000,1569400,
167888600),end=c(1550599,1560799,1565399,1571199,167888999),names=c("f
1","f2","f3","f4","f5")),strand= as.character("+"),space=c(6,6,6,6,5))
t1 =findOverlappingPeaks(peaks1, peaks2, maxgap=1000,
multiple=F,NameOfPeaks1="TF1", NameOfPeaks2="TF2")
peaks1withOverlap = t1$Peaks1withOverlaps
peaks1[ !rownames(peaks1) %in% rownames(peaks1withOverlap),]
peaks2withOverlap = t1$Peaks2withOverlaps
peaks2[ !rownames(peaks2) %in% rownames(peaks2withOverlap),]
Best regards,
Julie
On 1/14/11 3:24 PM, "Ron Hart" <rhart@rci.rutgers.edu> wrote:
Julie,
First off, thanks very much for providing the ChIPpeakAnno package in
R! Weve found it to be enormously useful and reasonably easy to use
(for us R neophytes)!
I have one question for you. I started to play with the
findOverlappingPeaks() function and I was wondering if youd
considered creating a similar function to generate intersections
instead of unions. In my case I want to know which subset of peaks
from condition #1 that do not overlap with those from condition #2. Or
those in #2 that dont overlap with #1.
It sounds to me as if I should be able to replace the findOverlaps()
function within your function with something like intersect() but I
dont think there is a version of intersect() specifically for ranged
data. Would this be difficult to create by modifying your function?
Thanks,
Ron
Ron Hart rhart@rci.rutgers.edu <mailto:rhart@rci.rutgers.edu>
W.M. Keck Center for Collaborative Neuroscience
<http: keck.rutgers.edu=""/> ,
Department of Cell Biology & Neuroscience <http: cbn.rutgers.edu=""/> ,
and Rutgers Stem Cell Research Center <http: scrc.rutgers.edu=""/>
Rutgers University
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