[BioC] Is a number within a set of ranges?

[Oleg Sklyar]

You would like to avoid loops here, especially nested loops: this is
what apply, sapply etc are for. Using your syntax:

final.presence = apply(gene, 1, function(x) any(x[2]>=place$start &
x[2]<=place$end))

-  
Dr Oleg Sklyar * EMBL-EBI, Cambridge CB10 1SD, UK * +441223494466


On Mon, 2007-10-29 at 12:42 -0500, Artur Veloso wrote:
> Hi Daniel,
> 
> I'm very new to R and I'm far from a good programmer, but I think that this
> small script should solve your problem. Well, at least for the example you
> provided it worked. I hope it helps.
> 
> Cheers,
> 
> Artur
> 
> > start <- c(1,5,13)
> > stop <- c(3,9,15)
> > place <- data.frame(start,stop)
> >
> > gene <- c(1,2,3,4)
> > position <- c(14,4,10,6)
> > position <- data.frame(gene,position)
> >
> > range <- list()
> > for(a in 1:dim(place)[1])
> + range[[a]] <- seq(place$start[a],place$stop[a])
> >
> > presence <- NULL
> > final.presence <- NULL
> > for(b in position$position)
> +     {
> +      for(c in 1:length(range))
> +             {
> +             presence <- c(presence,b%in%range[[c]])
> +             }
> +      final.presence <- c(final.presence,as.logical(sum(presence)))
> +      presence <- NULL
> +      }
> >
> > position[final.presence,]
>   gene position
> 1    1       14
> 4    4        6
> 
> 
> On 10/29/07, Daniel Brewer <daniel.brewer at icr.ac.uk> wrote:
> >
> > I have a table with a start and stop column which defines a set of
> > ranges.  I have another table with a list of genes with associated
> > position.  What I would like to do is subset the gene table so it only
> > contains genes whose position is within any of the ranges.  What is the
> > best way to do this?  The only way I can think of is to construct a long
> > list of conditions linked by ORs but I am sure there must be a better way.
> >
> > Simple example:
> >
> > Start   Stop
> > 1       3
> > 5       9
> > 13      15
> >
> > Gene    Position
> > 1       14
> > 2       4
> > 3       10
> > 4       6
> >
> > I would like to get out:
> > Gene    Position
> > 1       14
> > 4       6
> >
> > Any ideas?
> >
> > Thanks
> >
> > Dan
> >
> > --
> > **************************************************************
> > Daniel Brewer, Ph.D.
> > Institute of Cancer Research
> > Email: daniel.brewer at icr.ac.uk
> > **************************************************************
> >
> > The Institute of Cancer Research: Royal Cancer Hospital, a charitable
> > Company Limited by Guarantee, Registered in England under Company No. 534147
> > with its Registered Office at 123 Old Brompton Road, London SW7 3RP.
> >
> > This e-mail message is confidential and for use by the...{{dropped:13}}
> 
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