Re: [R] pairwise difference operator

From: Gabor Grothendieck <ggrothendieck_at_myway.com>
Date: Sat 31 Jul 2004 - 12:24:33 EST

Adaikalavan Ramasamy <ramasamy <at> cancer.org.uk> writes:

:
: There was a BioConductor thread today where the poster wanted to find
: pairwise difference between columns of a matrix. I suggested the slow
: solution below, hoping that someone might suggest a faster and/or more
: elegant solution, but no other response.
:
: I tried unsuccessfully with the apply() family. Searching the mailing
: list was not very fruitful either. The closest I got to was a cryptic
: chunk of code in pairwise.table().
:
: Since I do use something similar myself occasionally, I am hoping
: someone from the R-help list can suggest alternatives or past threads.
: Thank you.
:
: ### Code ###
: pairwise.difference <- function(m){
: npairs <- choose( ncol(m), 2 )
: results <- matrix( NA, nc=npairs, nr=nrow(m) )
: cnames <- rep(NA, npairs)
: if(is.null(colnames(m))) colnames(m) <- paste("col", 1:ncol(m), sep="")
:
: k <- 1
: for(i in 1:ncol(m)){
: for(j in 1:ncol(m)){
: if(j <= i) next;
: results[ ,k] <- m[ ,i] - m[ ,j]
: cnames[k] <- paste(colnames(m)[ c(i, j) ], collapse=".vs.")
: k <- k + 1
: }
: }
:
: colnames(results) <- cnames
: rownames(results) <- rownames(m)
: return(results)
: }
:
: ### Example using a matrix with 5 gene/row and 4 columns ###
: mat <- matrix( sample(1:20), nc=4 )
: colnames(mat) <- LETTERS[1:4]; rownames(mat) <- paste( "g", 1:5, sep="")
: mat
: A B C D
: g1 10 16 3 15
: g2 18 5 12 19
: g3 7 4 8 13
: g4 14 2 6 11
: g5 17 1 20 9
:
: pairwise.difference(mat)
: A.vs.B A.vs.C A.vs.D B.vs.C B.vs.D C.vs.D
: g1 -6 7 -5 13 1 -12
: g2 13 6 -1 -7 -14 -7
: g3 3 -1 -6 -4 -9 -5
: g4 12 8 3 -4 -9 -5
: g5 16 -3 8 -19 -8 11

  1. Note that mat[,j] - mat subtracts each column of mat from the j-th column so we just cbind 3 matrices:

      cbind( mat[,1]-mat[2:4], mat[,2]-mat[,3:4], mat[,3]-mat[,4,drop=F] )

2. For a general matrix a single sapply can do it like this:

      f <- function(i, mat) mat[, i-1] - mat[, i:ncol(mat), drop = FALSE]
      do.call("cbind", sapply(2:ncol(mat), f, mat))

3. To add nice column names just enhance f. The statements "z <- ..."

   and "do.call ..." are the same as before:

      f <- function(i, mat) {
         z <- mat[, i-1] - mat[, i:ncol(mat), drop = FALSE]
         colnames(z) <- paste(colnames(mat)[i-1], colnames(z), sep = "-")
         z
      }
      do.call("cbind", sapply(2:ncol(mat), f, mat))

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https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Received on Sat Jul 31 12:30:30 2004

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