[R] Near function?

[Wolfgang Huber]

Dear Bart,

"hclust" might be useful for this as well:

   dat = c(1,20,2,21)

   hc = hclust(dist(dat))

   thresh = 2
   ct = cutree(hc, h=thresh)

   clusteredNumbers = split(dat, ct)
   firstOne = dat[!duplicated(ct)]

 >  clusteredNumbers
$`1`
[1] 1 2
$`2`
[1] 20 21


 > firstOne
[1]  1 20


  Best wishes
   Wolfgang


> 
> I have an integer which is extracted from a dataframe, which is sorted by another column of the dataframe.
> Now I would like to remove some elements of the integer, which are near to others by their value. For example: integer: c(1,20,2,21) should be c(1,20).
> 
> I tried to write a function, but for some reason, somethings won't work
> 
> x <- 1:20
> near <- function(x,th) {
>     nr <- NROW(x)
>         for (i in 1:(nr-1)){
>         for (j in (i+1):nr){
>             if (j > nr) break
>             t=0
>             if (abs(x[i] - x[j]) < th) t = 1
>             if (t== 1) x <- x[-j]
>             if (t== 1) nr <- nr-1
>             if (t== 1) j <- (j-1)
>             cat (" i",i," j",j,"\n")
>             }} 
> x
> }
> near(x,10)
> 
> 
> This gives you 1  3  7 13 17 while I was suspecting 1, 20 as the outcome.
> If you look at the intermediate results of the cat instruction, you see that, after he substracted a number, he skipped the next one.
> 
> Sorting the integer is not an option, the order is important.
> I used an integer from 1:20 as an example, while x <- sample((1:20),20) is maybe a bit more representable for our data, but isn't reproducible for the output of the function.
> 
> Maybe there is already an R-function, which does such thing, or what is wrong with my coding?
> 
> 
> thanks a lot for your time
> 
> 
> Bart
> 	[[alternative HTML version deleted]]
> 
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-- 
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Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber