[Bioc-devel] vectorize default dist2 function in genefilter

[James F. Reid]

Dear bioc-devel,

the dist2 function in genefilter defined as:

dist2 <- function (x, fun = function(a, b) mean(abs(a - b), na.rm = 
TRUE), diagonal = 0) {

     if (!(is.numeric(diagonal) && (length(diagonal) == 1L)))
         stop("'diagonal' must be a numeric scalar.")
     res = matrix(diagonal, ncol = ncol(x), nrow = ncol(x))
     colnames(res) = rownames(res) = colnames(x)
     if (ncol(x) >= 2) {
         for (j in 2:ncol(x)) for (i in 1:(j - 1)) res[i, j] = res[j,
             i] = fun(x[, i], x[, j])
     }
     return(res)
}

could have it's default function vectorized as:

res <- apply(x, 2, function(i) colMeans(abs(x - i), na.rm=TRUE))

to improve performance for example in the ArrayQualityMetrics package.

Best.
James.