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    <p>Since the question originally had a tag 'bioinformatics' I'll mention the <a href="http://bioconductor.org" rel="nofollow noreferrer">Bioconductor</a> package <em><a href="http://bioconductor.org/packages/release/bioc/html/IRanges.html" rel="nofollow noreferrer">IRanges</a></em> (and it's companion for ranges on genomes <em><a href="http://bioconductor.org/packages/release/bioc/html/GenomicRanges.html" rel="nofollow noreferrer">GenomicRanges</a></em>)</p> <pre><code>&gt; library(IRanges) &gt; xx &lt;- c(1,1,1,1,1,1,0,0,0,0,1,1,1,1) &gt; sl = slice(Rle(xx), 1) &gt; sl Views on a 14-length Rle subject views: start end width [1] 1 6 6 [1 1 1 1 1 1] [2] 11 14 4 [1 1 1 1] </code></pre> <p>which could be coerced to a matrix, but that would often not be convenient for whatever the next step is</p> <pre><code>&gt; matrix(c(start(sl), end(sl)), ncol=2)      [,1] [,2] [1,]    1    6 [2,]   11   14 </code></pre> <p>Other operations might start on the <code>Rle</code>, e.g., </p> <pre><code>&gt; xx = c(2,2,2,3,3,3,0,0,0,0,4,4,1,1) &gt; r = Rle(xx) &gt; m = cbind(start(r), end(r))[runValue(r) != 0,,drop=FALSE] &gt; m [,1] [,2] [1,] 1 3 [2,] 4 6 [3,] 11 12 [4,] 13 14 </code></pre> <p><strong>See the help page <code>?Rle</code></strong> for the full flexibility of the <code>Rle</code> class; to go from a matrix like that above to a new Rle as asked in the comment below, one might create a new Rle of appropriate length and then subset-assign using an IRanges as index</p> <pre><code>&gt; r = Rle(0L, max(m)) &gt; r[IRanges(m[,1], m[,2])] = 1L &gt; r integer-Rle of length 14 with 3 runs Lengths: 6 4 4 Values : 1 0 1 </code></pre> <p>One could expand this to a full vector</p> <pre><code>&gt; as(r, "integer") [1] 1 1 1 1 1 1 0 0 0 0 1 1 1 1 </code></pre> <p>but often it's better to continue the analysis on the Rle. The class is very flexible, so one way of going from <code>xx</code> to an integer vector of 1's and 0's is</p> <pre><code>&gt; as(Rle(xx) &gt; 0, "integer") [1] 1 1 1 1 1 1 0 0 0 0 1 1 1 1 </code></pre> <p>Again, though, it often makes sense to stay in Rle space. And <a href="https://stackoverflow.com/questions/17121205/r-matrix-to-indexes/17121362#17121362">Arun</a>'s answer to your separate question is probably best of all.</p> <p><strong>Performance</strong> (speed) is important, although in this case I think the Rle class provides a lot of flexibility that would weigh against poor performance, and ending up at a matrix is an unlikely end-point for a typical analysis. Nonetheles the IRanges infrastructure <em>is</em> performant</p> <pre><code>eddi &lt;- function(xx) matrix(which(diff(c(0,xx,0)) != 0) - c(0,1), ncol = 2, byrow = TRUE) iranges = function(xx) { sl = slice(Rle(xx), 1) matrix(c(start(sl), end(sl)), ncol=2) } iranges.1 = function(xx) { r = Rle(xx) cbind(start(r), end(r))[runValue(r) != 0, , drop=FALSE] } </code></pre> <p>with</p> <pre><code>&gt; xx = sample(c(0, 1), 1e5, TRUE) &gt; microbenchmark(eddi(xx), iranges(xx), iranges.1(xx), times=10) Unit: milliseconds expr min lq median uq max neval eddi(xx) 45.88009 46.69360 47.67374 226.15084 234.8138 10 iranges(xx) 112.09530 114.36889 229.90911 292.84153 294.7348 10 iranges.1(xx) 31.64954 31.72658 33.26242 35.52092 226.7817 10 </code></pre>
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    1. COWhat if I have xx=c(2,2,2,3,3,3,0,0,0,0,4,4,1,1) and I want to get 1 3, 4 6, 11 12, and 13 14 in a 4x2 matrix?
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    2. CO@user1938809 I've added that to the response.
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    3. COMay I ask how to go from 1 3, 4 6, 11 12, and 13 14 to the vector form (1,1,1,1,1,1,0,0,0,0,1,1,1,1) without any loop assuming you know the vector size is 14. It is slow using loop. Thanks.
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