Hi James
I added your suggestion to the package, it is in svn revision 74349 and should
be on the server in the devel section soon.
This an old package - I noted the first commit to it had revision number 24 and
was by Robert Gentleman on 2001-08-01.
Best wishes
Wolfgang
El Mar 13, 2013, a las 10:41 am, James F. Reid <rei...@gmail.com> escribió:
> Hi Wolfgang,
>
> On 12/03/13 21:11, Wolfgang Huber wrote:
>>
>> Dear James
>>
>> Thank you. What would the saved time be (e.g. compared to the overall
>> runtime of arrayQualityMetrics)? I would be surprised if the saving was
>> worth the added complexity, but am always happy to be surprised.
>
> I believe so but maybe I'm missing something.
> Here are the system times on a 20000*100 on my laptop using just dist2, which
> would also have a consequence on the overall runtime of arrayQualityMetrics
> in aqm.heamap.
>
>
> dist2 <- function (x,
> fun = function(a, b) mean(abs(a - b), na.rm = TRUE),
> diagonal = 0) {
>
> defaultFun <- ifelse(missing(fun), TRUE, FALSE)
>
> 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) {
>
> if (defaultFun) {
> res <- apply(x, 2, function(i) colMeans(abs(x - i), na.rm=TRUE))
> } else {
> 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)
> }
>
> y <- matrix(rnorm(20000 * 100), 20000, 100)
>
> system.time(dist2(x = y, fun = function(a, b) mean(abs(a - b), na.rm=TRUE)))
> ## user system elapsed
> ## 11.664 0.060 11.800
>
> system.time(dist2(x = y))
> ## user system elapsed
> ## 5.201 0.348 5.600
>
> Not sure what you'd want to change to the Rd.
>
> Best,
> James.
>
>>
>> A patch of the .R and .Rd file would be most welcome and expedite the change.
>>
>> Btw, colSums apparently also works with 3-dim arrays, so both loops (over i
>> and j) could be vectorised, however afaIcs at the cost of constructing an
>> object of size nrow(x)^3 in memory, which might again break performance.
>>
>> Best wishes
>> Wolfgang
>>
>> Il giorno Mar 12, 2013, alle ore 4:43 PM, James F. Reid <rei...@gmail.com>
>> ha scritto:
>>
>>> 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.
>>>
>>> _______________________________________________
>>> Bioc-devel@r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
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