Thanks! guys for the help.
cheers!
Lee
On Wed, Oct 28, 2009 at 7:03 PM, Tony Plate <tpl...@acm.org> wrote:
> Here's a simple example that might help you get what you want:
>
> set.seed(1)
>> x <- matrix(rnorm(30), ncol=3, dimnames=list(NULL, letters[1:3]))
>> (xc <- cor(x))
>>
> a b c
> a 1.0000000 -0.3767034 -0.7158385
> b -0.3767034 1.0000000 0.6040273
> c -0.7158385 0.6040273 1.0000000
>
>> (cd <- data.frame(elt=outer(colnames(xc), colnames(xc), paste,
>> sep=":")[upper.tri(xc)], row=row(xc)[upper.tri(xc)],
>> col=col(xc)[upper.tri(xc)], cor=xc[upper.tri(xc)]))
>>
> elt row col cor
> 1 a:b 1 2 -0.3767034
> 2 a:c 1 3 -0.7158385
> 3 b:c 2 3 0.6040273
>
>> cd[order(-cd$cor),]
>>
> elt row col cor
> 3 b:c 2 3 0.6040273
> 1 a:b 1 2 -0.3767034
> 2 a:c 1 3 -0.7158385
>
>>
>>
> If you need something more efficient, try using which(..., arr.ind) to pick
> out matrix style indices, e.g.:
>
>> (ii <- which(xc > -0.4 & upper.tri(xc), arr.ind=T))
>>
> row col
> a 1 2
> b 2 3
>
>> cbind(ii, cor=xc[ii])
>>
> row col cor
> a 1 2 -0.3767034
> b 2 3 0.6040273
>
>>
>>
> -- Tony Plate
>
> Lee William wrote:
>
>> Hi! All,
>> I am working on a correlation matrix of 4217x4217 named 'cor_expN'. I wish
>> to obtain pairs with highest correlation values. So, I did this
>>
>>> b=matrix(data=NA,nrow=4217,ncol=1)
>>> rownames(b)=rownames(cor_expN)
>>> for(i in 1:4217){b[i,]=max(cor_expN[i,])}
>>> head(b)
>>>
>> [,1]
>> aaeA_b3241_14 0.7181912
>> aaeB_b3240_15 0.7513084
>> aaeR_b3243_15 0.7681684
>> aaeX_b3242_12 0.5230587
>> aas_b2836_14 0.6615927
>> aat_b0885_14 0.6344144
>>
>> Now I want the corresponding columns for the above values. For that I
>> tried
>> this
>>
>>> c=matrix(data=NA,nrow=4217,ncol=1)
>>> for(i in 1:4217){b[i,]=colnames(max(cor_expN[i,]))}
>>>
>>
>> And got the following error:
>> Error in b[i, ] = colnames(max(cor_expN[i, ])) : number of items to
>> replace
>> is not a multiple of replacement length
>> Any thoughts?
>>
>> Lee
>>
>> [[alternative HTML version deleted]]
>>
>>
>> ______________________________________________
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>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>>
>
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