[R] Still avoiding loops

[Jacques VESLOT]

It is part of a function to determine Dice's index in the framewok of AFLP
analysis.

X is a binary matrix which value for each strain (lines) and each base pair
(columns) is 1 where there is a peak and 0 where there is no peak as
biologists explained to me.

The first step is to compare each strain with one another by counting the
number of 0, 1 and 2, respectively where there is no peak, one peak or 2
peaks for each base pair.

In that respect, I want to add together each pair of X's lines.

For the moment, there is a double loop calculating, at each step, the sum of
two lines as a vector Y and counting the number of 0, 1 and 2 in it for
inclusion in other operations.

I read your posting...

Thanks for helping,

Jacques VESLOT


-----Message d'origine-----
De : Adaikalavan Ramasamy [mailto:ramasamy at cancer.org.uk]
Envoyé : mercredi 26 janvier 2005 15:57
À : jacques.veslot at cirad.fr
Cc : R-help
Objet : Re: [R] Still avoiding loops


Please give a simple example of the input data and output that you
desire. It is difficult to understand from you partial codes what you
mean. For example what is Y ?

Are you trying to find add values from pairs of rows ? If so, please see
my posting "pairwise difference operator" where I wanted to find the
differences between pairs of columns.
http://tolstoy.newcastle.edu.au/R/help/04/07/1633.html

Otherwise, please send a sample input and output. Thank you.

Regards, Adai


On Wed, 2005-01-26 at 11:40 +0400, Jacques VESLOT wrote:
> Dear all,
>
> I have a matrix X with 47 lines and say 500 columns - values are in {0,1}.
> I'd like to compare lines.
>
> For that, I first did:
>
> for (i in 1:(dim(X)[1]-1))
> for (j in (i+1):dim(X)[1]) {
> 	Y <- X[i,]+Y[j,]
> 	etc.
>
> but, since it takes a long time, I would prefer avoding loops;
> for that, my first idea was to add this matrix:
>
> X1=X[,rep(1:46,46:1)]
>
> to this one:
>
> res=NULL
> for (i in (2:47)) res=c(res,i:47)
>
> X2=X[,res]
>
> (Is it a nice alternative way ?)
> Is there a way to create the second matrix X2 without a loop, such as for
X1
> ?
>
> Thanks in advance,
>
> Jacques VESLOT
>
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