[Bioc-devel] How to speed up GRange comparision

[Pages, Herve]

On 1/29/20 23:31, web working wrote:
> Hi Herve,
> 
> Thank you for your answer. pcompare works fine for me. Here my solution:
> 
> query <- GRanges(rep("chr1", 4), IRanges(c(1, 5, 9, 20), c(2, 6, 10, 22)))
> subject <- GRanges(rep("chr1",4), IRanges(c(3, 1, 1, 15), c(4, 2, 2, 21)))
> out <- vector("numeric", length(query))
> out[(which(abs(pcompare(query, subject))<5))] <- 1
> out

Why not just

   out <- abs(pcompare(query, subject)) < 5

In any case you should use integer instead of numeric (twice more 
compact in memory).

H.

> 
> Carey was right that this here is off list. Next time I will pose my 
> question on support.bioconductor.org 
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__support.bioconductor.org&d=DwMCaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=VZ2-jg7W_Ctrav2BpPVUPpvJlyISX3QVwFAzTnDnNTs&s=Jdmp3dD6ubzPdE8KjFJ3urOav62YTOmxYcYZ4000MY8&e=>.
> 
> Best,
> 
> Tobias
> 
> Am 29.01.20 um 18:02 schrieb Pages, Herve:
>> Yes poverlaps().
>>
>> Or pcompare(), which should be even faster. But only if you are not
>> afraid to go low-level. See ?rangeComparisonCodeToLetter for the meaning
>> of the codes returned by pcompare().
>>
>> H.
>>
>> On 1/29/20 08:01, Michael Lawrence via Bioc-devel wrote:
>>> poverlaps()?
>>>
>>> On Wed, Jan 29, 2020 at 7:50 AM web working<webworking using posteo.de>  wrote:
>>>> Hello,
>>>>
>>>> I have two big GRanges objects and want to search for an overlap of  the
>>>> first range of query with the first range of subject. Then take the
>>>> second range of query and compare it with the second range of subject
>>>> and so on. Here an example of my problem:
>>>>
>>>> # GRanges objects
>>>> query <- GRanges(rep("chr1", 4), IRanges(c(1, 5, 9, 20), c(2, 6, 10,
>>>> 22)), id=1:4)
>>>> subject <- GRanges(rep("chr1",4), IRanges(c(3, 1, 1, 15), c(4, 2, 2,
>>>> 21)), id=1:4)
>>>>
>>>> # The 2 overlaps at the first position should not be counted, because
>>>> these ranges are at different rows.
>>>> countOverlaps(query, subject)
>>>>
>>>> # Approach 1 (bad style. I have simplified it to understand)
>>>> dat <- as.data.frame(findOverlaps(query, subject))
>>>> indexDat <- apply(dat, 1, function(x) x[1]==x[2])
>>>> indexBool <- dat[indexDat,1]
>>>> out <- rep(FALSE, length(query))
>>>> out[indexBool] <- TRUE
>>>> as.numeric(out)
>>>>
>>>> # Approach 2 (bad style and takes too long)
>>>> out <- vector("numeric", 4)
>>>> for(i in seq_along(query)) out[i] <- (overlapsAny(query[i], subject[i]))
>>>> out
>>>>
>>>> # Approach 3 (wrong results)
>>>> as.numeric(overlapsAny(query, subject))
>>>> as.numeric(overlapsAny(split(query, 1:4), split(subject, 1:4)))
>>>>
>>>>
>>>> Maybe someone has an idea to speed this up?
>>>>
>>>>
>>>> Best,
>>>>
>>>> Tobias
>>>>
>>>> _______________________________________________
>>>> Bioc-devel using r-project.org  mailing list
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>>>

-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
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