Hello,
I'm glad it helped. Now to make the result readable. (I had thought of it.)
pairwise.ratios <- function(x, prefix="probeset", char=":"){
n <- ncol(x)
cn <- colnames(x)
if(length(cn) == 0){
cn <- gsub(" ", "0", formatC(seq.int(n), width=nchar(n)))
cn <- paste(prefix, cn, sep="")
}
cmb <- combn(n, 2)
r1 <- apply(cmb, 2, function(j) x[, j[1]]/x[, j[2]])
r2 <- apply(cmb, 2, function(j) x[, j[2]]/x[, j[1]])
colnames(r1) <- apply(cmb, 2, function(j) paste(cn[j], collapse=char))
colnames(r2) <- apply(cmb, 2, function(j) paste(cn[rev(j)],
collapse=char))
cbind(r1, r2)[, order(c(colnames(r1), colnames(r2)))]
}
m1 <- matrix(1:24, ncol=6)
pairwise.ratios(m1)
Rui Barradas
genome1976 wrote
>
> Thanks so much Rui. I really appreciate all the help.
>
> I implemented the code and it ran fine. I was wondering how I could
> include the probeset ids as probeset1:probeset2 in the final output so
> that I know which ratios are for which probeset pairs.
>
>
> Thanks so much.
> Som.
> Date: Sat, 12 May 2012 09:29:54 -0700
> From: ml-node+s789695n4629105h16@.nabble
> To: genome1976@
> Subject: Re: Calculating all possible ratios
>
>
>
> Hello,
>
>
> If by all possible gene ratios you mean all pairwise column ratios, try
>
> the following.
>
>
> # Make up some data
>
> x <- matrix(1:24, ncol=6)
>
>
> cmb <- combn(ncol(x), 2)
>
> r1 <- apply(cmb, 2, function(j) x[, j[1]]/x[, j[2]])
>
> r2 <- apply(cmb, 2, function(j) x[, j[2]]/x[, j[1]])
>
> cbind(r1, r2)
>
>
> Note that the dataset must be a numeric only matrix or data.frame.
>
>
> Hope this helps,
>
>
> Rui Barradas
>
>
> Em 12-05-2012 11:00, [hidden email] escreveu:
>
>> Date: Fri, 11 May 2012 12:39:23 -0700 (PDT)
>
>> From: genome1976<[hidden email]>
>
>> To:[hidden email]
>
>> Subject: [R] Calculating all possible ratios
>
>> Message-ID:<[hidden email]>
>
>> Content-Type: text/plain
>
>>
>
>> I have a data matrix with genes as columns and samples as rows. I want
>> to
>
>> create all possible gene ratios.Is there an elegant and fast way to do it
>> in
>
>> R and write it to a dataframe?
>
>>
>
>> Thanks for any help.
>
>> Som.
>
>>
>
>> --
>
>> View this message in
>> context:http://r.789695.n4.nabble.com/Calculating-all-possible-ratios-tp4627405.html
>> Sent from the R help mailing list archive at Nabble.com.
>
>> [[alternative HTML version deleted]]
>
>>
>
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