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<webwork...@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@r-project.org mailing list >>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=FSrHBK59_OMc6EbEtcPhkTVO0cfDgSbQBGFOXWyHhjc&s=3tZpvRAw7T5dP21u32TRTf4lZ4QFLtmkouKR7TUlJws&e= >>> -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fredhutch.org Phone: (206) 667-5791 Fax: (206) 667-1319 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel