R help - Aug 2008 - sequence with start and stop positions

Hi,

I have a vector of start positions, and another vector of stop positions,

eg start<-c(1,20,50)
     stop<-c(7,25,53)

Is there a quick way to create a sequence from these vectors?

new<-c(1,2,3,4,5,6,7,20,21,22,23,24,25,50,51,52,53)

the way Im doing it at the moment is

pos<-seq(start[1],stop[1])

for (i in 2:length(start)){
  new<-seq(start[i],stop[i])
  pos<-c(pos,new)
}

This works on small data, but its very inefficient on large vectors, and 
is taking forever!

Anybody no a better way?

many thanks,
Chris

There's a kind of way, but it may be more 'elegant' than fast for
large sequences
> start <- c(1,20,50)
> stop <- c(7,25,53)
> unlist(mapply(Vectorize(seq), start, stop))
 [1]  1  2  3  4  5  6  7 20 21 22 23 24 25 50 51 52 53

Bill Venables
http://www.cmis.csiro.au/bill.venables/


-----Original Message-----
From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org]
On Behalf Of Chris Oldmeadow
Sent: Tuesday, 26 August 2008 2:42 PM
To: r-help at r-project.org
Subject: [R] sequence with start and stop positions

Hi,

I have a vector of start positions, and another vector of stop positions,

eg start<-c(1,20,50)
     stop<-c(7,25,53)

Is there a quick way to create a sequence from these vectors?

new<-c(1,2,3,4,5,6,7,20,21,22,23,24,25,50,51,52,53)

the way Im doing it at the moment is

pos<-seq(start[1],stop[1])

for (i in 2:length(start)){
  new<-seq(start[i],stop[i])
  pos<-c(pos,new)
}

This works on small data, but its very inefficient on large vectors, and
is taking forever!

Anybody no a better way?

many thanks,
Chris

______________________________________________
R-help at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Try:
> unlist(mapply(seq, c(1,20,50), c(7,25,53)))
 [1]  1  2  3  4  5  6  7 20 21 22 23 24 25 50 51 52 53

-Christos 
> -----Original Message-----
> From: r-help-bounces at r-project.org 
> [mailto:r-help-bounces at r-project.org] On Behalf Of Chris Oldmeadow
> Sent: Tuesday, August 26, 2008 12:42 AM
> To: r-help at r-project.org
> Subject: [R] sequence with start and stop positions
> 
> Hi,
> 
> I have a vector of start positions, and another vector of 
> stop positions,
> 
> eg start<-c(1,20,50)
>      stop<-c(7,25,53)
> 
> Is there a quick way to create a sequence from these vectors?
> 
> new<-c(1,2,3,4,5,6,7,20,21,22,23,24,25,50,51,52,53)
> 
> the way Im doing it at the moment is
> 
> pos<-seq(start[1],stop[1])
> 
> for (i in 2:length(start)){
>   new<-seq(start[i],stop[i])
>   pos<-c(pos,new)
> }
> 
> This works on small data, but its very inefficient on large 
> vectors, and is taking forever!
> 
> Anybody no a better way?
> 
> many thanks,
> Chris
> 
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide 
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
> 
>

And somewhat faster still (YMMV):

unlist(mapply(":", start, stop))

HTH,
Ray Brownrigg
Victoria University of Wellington

Christos Hatzis wrote:
> Try:
> 
>> unlist(mapply(seq, c(1,20,50), c(7,25,53)))
>  [1]  1  2  3  4  5  6  7 20 21 22 23 24 25 50 51 52 53
> 
> -Christos 
> 
>> -----Original Message-----
>> From: r-help-bounces at r-project.org 
>> [mailto:r-help-bounces at r-project.org] On Behalf Of Chris Oldmeadow
>> Sent: Tuesday, August 26, 2008 12:42 AM
>> To: r-help at r-project.org
>> Subject: [R] sequence with start and stop positions
>>
>> Hi,
>>
>> I have a vector of start positions, and another vector of 
>> stop positions,
>>
>> eg start<-c(1,20,50)
>>      stop<-c(7,25,53)
>>
>> Is there a quick way to create a sequence from these vectors?
>>
>> new<-c(1,2,3,4,5,6,7,20,21,22,23,24,25,50,51,52,53)
>>
>> the way Im doing it at the moment is
>>
>> pos<-seq(start[1],stop[1])
>>
>> for (i in 2:length(start)){
>>   new<-seq(start[i],stop[i])
>>   pos<-c(pos,new)
>> }
>>
>> This works on small data, but its very inefficient on large 
>> vectors, and is taking forever!
>>
>> Anybody no a better way?
>>
>> many thanks,
>> Chris
>>
>> ______________________________________________
>> R-help at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide 
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>>
> 
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

On Tue, 26 Aug 2008, Chris Oldmeadow wrote:
> Hi,
>
> I have a vector of start positions, and another vector of stop positions,
>
> eg start<-c(1,20,50)
>     stop<-c(7,25,53)
>
> Is there a quick way to create a sequence from these vectors?
>
> new<-c(1,2,3,4,5,6,7,20,21,22,23,24,25,50,51,52,53)

Vectorize the process.
> start2 <- rep( start, stop-start+1 )
> lens <- stop-start+1
> offset <- rep(cumsum(c( 0, lens )),c( lens ,0 ))
> seq(along=offset)-offset+start2-1
  [1]  1  2  3  4  5  6  7 20 21 22 23 24 25 50 51 52 53
>
HTH,

Chuck
>
> the way Im doing it at the moment is
>
> pos<-seq(start[1],stop[1])
>
> for (i in 2:length(start)){
>  new<-seq(start[i],stop[i])
>  pos<-c(pos,new)
> }
>
> This works on small data, but its very inefficient on large vectors, and is
> taking forever!
>
> Anybody no a better way?
>
> many thanks,
> Chris
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
Charles C. Berry                            (858) 534-2098
                                             Dept of Family/Preventive Medicine
E mailto:cberry at tajo.ucsd.edu	            UC San Diego
http://famprevmed.ucsd.edu/faculty/cberry/  La Jolla, San Diego 92093-0901