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

[Christos Hatzis]

> pos <- matrix(c(1, 5, 13, 3, 9, 15), ncol=2) pos
     [,1] [,2]
[1,]    1    3
[2,]    5    9
[3,]   13   15
> gene.pos <- c(14,4,10,6)
> gene.pos
[1] 14  4 10  6

> within <- sapply(gene.pos, function(g) any(apply(pos, 1, function(x)
findInterval(g, x)) == 1))

> gene.pos[within]
[1] 14  6 

Look at ?findInterval, which does all the work.  It returns 1 if within
range in this case.

-Christos 

> -----Original Message-----
> From: bioconductor-bounces at stat.math.ethz.ch 
> [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of 
> Daniel Brewer
> Sent: Monday, October 29, 2007 12:29 PM
> To: bioconductor at stat.math.ethz.ch
> Subject: [BioC] Is a number within a set of ranges?
> 
> 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 
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> 
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