On 1/29/20 08:04, Jianhong Ou, Ph.D. wrote: > Try > dist=distance(query, subject) > dist==0 > ?
Please be aware that dist==0 does NOT mean that 2 ranges overlap. It means that they overlap OR are **adjacent**: > distance(GRanges("chr1:1-20"), GRanges("chr1:21-25")) [1] 0 H. > > On 1/29/20, 10:50 AM, "Bioc-devel on behalf of web working" > <bioc-devel-boun...@r-project.org on behalf of 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=DwIDaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=PXg851DHXyo-Gs3eMIfeo49gUXVh-JSZu_MZDDxGun8&m=CL_4pe8tWi75jDizROxriMm7-LhebnosKRxforvK2Jo&s=Ft0x9f_4tOy2Ov9DHVp5KlTOSI4CeURNB8ywlrwgn9E&e= > > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=mlMbcbdMyysqzyTia1k6Xb4YO7x7jyDtw2bT7ad0dyg&s=jPRTi7pxhHzcFnU-du42SSiHfemeYcUdEF4RZfqdCvU&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