[R] Still avoiding loops

[Liaw, Andy]

> From: Robert Kruus
> 
> Slight edit?

Yes.  Thank you. Jacques caught that as well...

Andy
 
> --------
> 
> It is  rumored that on Wed, 26 Jan 2005 09:24:44 -0500
> "Liaw, Andy" <andy_liaw at merck.com> wrote:
> 
> > See if this does what you want:
> > 
> > > m <- matrix(round(runif(24)), 4, 6)  # simulate some data
> > > m
> >      [,1] [,2] [,3] [,4] [,5] [,6]
> > [1,]    0    1    0    1    0    1
> > [2,]    0    1    1    1    0    0
> > [3,]    1    1    1    0    0    0
> > [4,]    1    0    0    0    1    0
> > > library(gtools)  # Install the gregmisc package if you don't have
> > > it. idx <- combinations(nrow(m), 2)
> > > res <- m[idx[,1],] + m[idx[,2]]
> 
> I think you missed a "," (if you want pairwise row sums)
> res <- m[idx[,1],] + m[idx[,2],]
> 
> > > rownames(res) <- paste(idx[,1], idx[,2], sep="+")
> > > res
> >     [,1] [,2] [,3] [,4] [,5] [,6]
> > 1+2    0    1    0    1    0    1
> > 1+3    1    2    1    2    1    2
> > 1+4    1    2    1    2    1    2
> > 2+3    1    2    2    2    1    1
> > 2+4    1    2    2    2    1    1
> > 3+4    2    2    2    1    1    1
> > 
> > Andy
> >  
> > 
> > > From: 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
> > > >
> > > > ______________________________________________
> > > > R-help at stat.math.ethz.ch mailing list
> > > > https://stat.ethz.ch/mailman/listinfo/r-help
> > > > PLEASE do read the posting guide!
> > > http://www.R-project.org/posting-guide.html
> > > >
> > > 
> > > ______________________________________________
> > > R-help at stat.math.ethz.ch mailing list
> > > https://stat.ethz.ch/mailman/listinfo/r-help
> > > PLEASE do read the posting guide! 
> > > http://www.R-project.org/posting-guide.html
> > > 
> > >
> > 
> > ______________________________________________
> > R-help at stat.math.ethz.ch mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide!
> > http://www.R-project.org/posting-guide.html
> > 
> 
> 
> --------
> 
> -- 
> robert.kruus at utoronto.ca
> "There are ten church members by inheritance for every one by
> conviction."                           [Anonymous]
> t
> 
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide! 
> http://www.R-project.org/posting-guide.html
> 
>