On 1/29/20 13:14, Jianhong Ou, Ph.D. wrote:
> Oh, I forget that. Thank you for reminder.
> Then how about:
>
> distance(query, narrow(subject, start=2, end=-2)) == 0
>
> ?
Yep, that's more accurate. With the following gotcha:
'narrow(subject, start=2, end=-2)' will fail if 'subject'
contains ranges that cover less than 2 positions
Not an unlikely situation e.g. if 'subject' contains TSS!
I just feel that distance() is not really appropriate to detect overlaps.
H.
>
>
> On 1/29/20, 12:40 PM, "Pages, Herve" <hpa...@fredhutch.org> wrote:
>
> 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
>
>
--
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
