[R] pattern search

[Prof Brian Ripley]

On Fri, 29 Oct 2004, Sean Liang wrote:

> Thanks for getting back to me. My situation is a bit more complicated.
> I have a vector of sequences each of which might contain any number of a
> given pattern (e.g.
> 
> >pat=c("ATCGTTTGCTAC", "GGCTAATGCATTGC");
> > grep ("TGC", pat)
> [1] 1 2
> 
> grep only tells me the position of first occurrence in each element
> whereas the second element contains two "TGC"s. 

sapply(strsplit(paste(1,pat,2, sep=""), "TGC"), length)-1

and you can also figure out the positions.

You can also do it recursively with regexpr (on the same page as grep, no 
less).

-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595