[BioC] How to write a text file of a pamr.confusion table ?

[Björn Usadel]

Hi Giulio,

you might try sink for diverting the output.

Otherwise,....
Having a look at pamr.confusion (> pamr.confusion on the command line)
shows that only if the parameter extra is set to false you get a 
confusion matrix returned.
So either you set it extra to False, or you redefine the function

pamr.Konfusion<- function (fit, threshold, extra = TRUE)
{
    ii <- (1:length(fit$threshold))[fit$threshold >= threshold]
    ii <- ii[1]
    predicted <- fit$yhat[, ii]
    if (!is.null(fit$y)) {
        true <- fit$y[fit$sample.subset]
        tt <- table(true, predicted)
    }
    else {
        true <- fit$proby[fit$sample.subset, ]
        ytemp <- apply(true, 1, which.is.max)
        temp <- c(predicted, names(table(ytemp)))
        nams <- names(table(temp))
        Yhat <- model.matrix(~factor(temp) - 1, data = list(y = temp))
        Yhat <- Yhat[1:length(predicted), ]
        tt <- matrix(NA, nrow = length(fit$prior), ncol = length(fit$prior))
        for (i in 1:length(fit$prior)) {
            for (j in 1:length(fit$prior)) {
                tt[i, j] <- sum(true[, i] * Yhat[, j])
            }
        }
        dimnames(tt) <- list(names(table(ytemp)), nams)
    }

if (extra) {
        tt1 <- tt
        diag(tt1) <- 0
        tt <- cbind(tt, apply(tt1, 1, sum)/apply(tt, 1, sum))
        dimnames(tt)[[2]][ncol(tt)] <- "Class Error rate"
       print(tt)    #<-****can go
        cat(c("Overall error rate=", round(sum(tt1)/sum(tt),
            3)), fill = TRUE)
       return(tt)  # <-**** add this
 }
    if (!extra) {
        return(tt)
    }
}


Cheers,
Björn

>Hi,
>
>really I hope this is not a stupid question. I would like to write a text 
>file with the output of  pamr.confusion function. Obviously I tried first 
>with the usual
>
>  
>
>>write.table(file="test.txt",pamr.confusion(mysamplespamtrain, thr))
>>    
>>
>   K  N Class Error rate
>K 26  4        0.1333333
>N  2 23        0.0800000
>Overall error rate= 0.109
>
>but all I write is an empty file. The same with "write" or assigning 
>pamr.confusion to a variable (pc <- pamr.confusion(.....) ).
>I also tried changing the device, to write a jpeg or whatelse; I tried to 
>play with Device related commands. No way. I followed James McDonald 
>suggestion
>found in the mail archive.
>
>  
>
>>pamr.confusion(mData.results, threshold=4.0)
>>    
>>
>(table)
>  
>
>>savePlot("Confusion", "wmf")
>>    
>>
>Error in savePlot("Confusion", "wmf") : no such device (...well, there's no 
>graph device...).
>
>Anyway, there's anyone who has some hints ? I think that maybe is a simple 
>command, but I don't know how to do it.
>
>Thanks in advance, and sorry if is a too banal question...
>
>Giulio
>
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