R help - Sep 2005 - Finding all overlaps between two sets of 1-Dimensional regions

I have a simply defined regions ([start,end] where start<end).  I have two
large sets of them and want to find all regions in the first that overlap
any regions in the second.  The closest I could find by searching is
overlap.owin in I can do this by looping, but there is likely a better way
to do this.  Any suggestions?

Thanks,
Sean

maybe something like this could work in your case:

set1 <- t(apply(matrix(rnorm(20), 10, 2), 1, sort))
set2 <- t(apply(matrix(rnorm(10), 5, 2), 1, sort))
########################
set1. <- apply(set1, 1, rev)
apply(set2, 1, function(x) apply(set1. <= x, 2, any))


I hope it helps.

Best,
Dimitris

----
Dimitris Rizopoulos
Ph.D. Student
Biostatistical Centre
School of Public Health
Catholic University of Leuven

Address: Kapucijnenvoer 35, Leuven, Belgium
Tel: +32/16/336899
Fax: +32/16/337015
Web: http://www.med.kuleuven.be/biostat/
     http://www.student.kuleuven.be/~m0390867/dimitris.htm


----- Original Message ----- 
From: "Sean Davis" <sdavis2 at mail.nih.gov>
To: "r-help" <r-help at stat.math.ethz.ch>
Sent: Friday, September 02, 2005 3:17 PM
Subject: [R] Finding all overlaps between two sets of 1-Dimensional 
regions

>I have a simply defined regions ([start,end] where start<end).  I 
>have two
> large sets of them and want to find all regions in the first that 
> overlap
> any regions in the second.  The closest I could find by searching is
> overlap.owin in I can do this by looping, but there is likely a 
> better way
> to do this.  Any suggestions?
>
> Thanks,
> Sean
>
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide! 
> http://www.R-project.org/posting-guide.html
> 

Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm

On Fri, 2 Sep 2005, Sean Davis wrote:
> I have a simply defined regions ([start,end] where start<end).  I have
two
> large sets of them and want to find all regions in the first that overlap
> any regions in the second.  The closest I could find by searching is
> overlap.owin in I can do this by looping, but there is likely a better way
> to do this.  Any suggestions?

findInterval can be helpful and fast for larger problems

Say s1,e1 (>0) are the starts and ends of your first set and s2,e2 (>0) 
are for the second and are in order according to s2 .

I think this is what you need to get going:

s2.0 <- c(0, s2) # if any s1 < any s2, this is needed
e2.0 <- c(0, e2)

s1.in.int <- s1 <= e.2.0 [ findInterval( s1, s2.0 ) ]
e1.in.same.int <- e1 <= e.2.0 [ findInterval( s1, s2.0 ) ]

e1.in.any.int <- e1 <= e.2.0 [ findInterval( e1, s2.0 ) ]

Caveat: Possible typos above

Chuck
>
> Thanks,
> Sean
>
>
>
Charles C. Berry                        (858) 534-2098
                                          Dept of Family/Preventive Medicine
E mailto:cberry at tajo.ucsd.edu	         UC San Diego
http://biostat.ucsd.edu/~cberry/         La Jolla, San Diego 92093-0717