R help - Jan 2010 - Function for describing segements in sequential data

Dear R-users,

Say that I have a sequence of zeroes and ones:

x <- c(1,1,1,0,0,0,0,1,1,1,0,0,0,0,1,1,1,0,0,0,0)

The sequences of ones represent segments and I want to report the starting and
endpoints of these segments. For example, in 'x', the first segment
starts at location 1 and ends at 3, and the second segment starts at location 8
and ends at location 10. Is there an efficient way of doing this in R without
having to right a bunch of if-else conditions? I know the rle function will
report the length of the segments but not the endpoints.

Thanks in advance.

Gregory Gentlemen



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> -----Original Message-----
> From: r-help-bounces at r-project.org 
> [mailto:r-help-bounces at r-project.org] On Behalf Of Gregory Gentlemen
> Sent: Wednesday, January 27, 2010 9:31 AM
> To: r-help at r-project.org
> Subject: [R] Function for describing segements in sequential data
> 
> Dear R-users,
> 
> Say that I have a sequence of zeroes and ones:
> 
> x <- c(1,1,1,0,0,0,0,1,1,1,0,0,0,0,1,1,1,0,0,0,0)
> 
> The sequences of ones represent segments and I want to report 
> the starting and endpoints of these segments. For example, in 
> 'x', the first segment starts at location 1 and ends at 3, 
> and the second segment starts at location 8 and ends at 
> location 10. Is there an efficient way of doing this in R 
> without having to right a bunch of if-else conditions? I know 
> the rle function will report the length of the segments but 
> not the endpoints.
You can use expressions based on cumsum(rle(x)$lengths) or, more
directly, on the following functions 
   isFirstInRun <- function(x)c(TRUE, x[-1]!=x[-length(x)])
   isLastInRun <- function(x)c(x[-1]!=x[-length(x)], TRUE)
which do part of what rle() does.  E.g.,
   > which(isFirstInRun(x) & x==1) # starting positions of runs of
1's
   [1]  1  8 15
   > which(isLastInRun(x) & x==1) # ending positions of runs of 1's
   [1]  3 10 17

Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com 
 
> 
> Thanks in advance.
> 
> Gregory Gentlemen
> 
> 
> 
>       
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> ______________________________________________
> R-help at r-project.org mailing list
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> PLEASE do read the posting guide 
> http://www.R-project.org/posting-guide.html
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>

Hi,

On Wed, Jan 27, 2010 at 12:31 PM, Gregory Gentlemen
<gregory_gentlemen at yahoo.ca> wrote:
> Dear R-users,
>
> Say that I have a sequence of zeroes and ones:
>
> x <- c(1,1,1,0,0,0,0,1,1,1,0,0,0,0,1,1,1,0,0,0,0)
>
> The sequences of ones represent segments and I want to report the starting
and endpoints of these segments. For example, in 'x', the first segment
starts at location 1 and ends at 3, and the second segment starts at location 8
and ends at location 10. Is there an efficient way of doing this in R without
having to right a bunch of if-else conditions?
How about something like this:

start <- which(diff(c(0,x)) == 1)  ## Append first 0 for a
"bookend"
end <- which(diff(x) == -1)

start is: 1, 8, 15
end is: 3, 10, 17

-steve

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact

On Wed, 27 Jan 2010, Gregory Gentlemen wrote:
> Dear R-users,
>
> Say that I have a sequence of zeroes and ones:
>
> x <- c(1,1,1,0,0,0,0,1,1,1,0,0,0,0,1,1,1,0,0,0,0)
>
> The sequences of ones represent segments and I want to report the 
> starting and endpoints of these segments. For example, in 'x', the
first
> segment starts at location 1 and ends at 3, and the second segment 
> starts at location 8 and ends at location 10. Is there an efficient way 
> of doing this in R without having to right a bunch of if-else 
> conditions? I know the rle function will report the length of the 
> segments but not the endpoints.
If this is more than a small one-off problem you might try this:
> require(IRanges) # from BioConductor
> IRanges(Rle(x)==1) # n.b. Rle != rle
IRanges of length 3
     start end width
[1]     1   3     3
[2]     8  10     3
[3]    15  17     3
>

HTH,

Chuck
>
> Thanks in advance.
>
> Gregory Gentlemen
>
>
>
>      __________________________________________________________________
> [[elided Yahoo spam]]
>
>
> 	[[alternative HTML version deleted]]
>
> ______________________________________________
> 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