Hi Dario,
You can try to use 'successiveIRanges(runLength(qrle))' instead
of 'as(qrle, "IRanges")'.
Cheers,
H.
On 06/25/2010 01:05 AM, Dario Strbenac wrote:
That's a neat and elegant idea, but it's not actually possible to do the
following part
as(qrle, "IRanges")
Error in asMethod(object) :
cannot coerce a non-logical 'Rle' or a logical 'Rle' with NAs to an IRanges
object
Thanks,
Dario.
---- Original message ----
Date: Thu, 24 Jun 2010 23:53:08 -0700
From: Michael Lawrence<[email protected]>
Subject: Re: [Bioc-sig-seq] Finding Mean Value of Overlapping Ranges
To: [email protected]
Cc: [email protected]
On Thu, Jun 24, 2010 at 10:31 PM, Dario Strbenac
<[email protected]> wrote:
Hello,
I have a question about what is the most efficient
way to perform my use case.
What I have done is gotten a matchMatrix from an
overlapping, then split it :
regionSiteMap<- findOverlaps(regions,
sites)@matchMatrix
indexList<- split(regionSiteMap[, "subject"],
regionSiteMap[, "query"])
Instead of splitting, get the scores and query hits
into an Rle:
ol<- findOverlaps(regions, sites)
srle<- Rle(scoreVec[subjectHits(ol)])
qrle<- Rle(queryHits(ol))
The Rle compression may not be appropriate for your
scores, but now you can use the query Rle to define
Views on the score Rle:
v<- Views(srle, as(qrle, "IRanges"))
Now all the view methods are at your disposal, like
viewMeans():
means<- viewMeans(v)
Michael
Now I'd like to, for each region, use the indices
to the sites to get the sites' scores from a
vector and take the mean, like :
means<- sapply(indicesList, function(indices)
mean(scoreVect[indices]))
The problem about this is that I have ~ 8 million
'regions', and ~ 28 million 'sites'. So the
indexList is a list of ~ 8 million elements with a
few indices in each one, and scoresVect is a
numeric vector of scores of length ~ 28 million.
Can anyone suggest what is the fastest way to go
on this task ?
--------------------------------------
Dario Strbenac
Research Assistant
Cancer Epigenetics
Garvan Institute of Medical Research
Darlinghurst NSW 2010
Australia
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--------------------------------------
Dario Strbenac
Research Assistant
Cancer Epigenetics
Garvan Institute of Medical Research
Darlinghurst NSW 2010
Australia
_______________________________________________
Bioc-sig-sequencing mailing list
[email protected]
https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
_______________________________________________
Bioc-sig-sequencing mailing list
[email protected]
https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
