search for: promotergen

Displaying 5 results from an estimated 5 matches for "promotergen".

Did you mean: promotergene
2008 Jun 25
1
stringdot
Hi!! I am trying to figure out how to use the string kernel "stringdot" in kernlab. k <- function(x,y) { (sum(x*y) +1)*exp(-0.001*sum((x-y)^2)) } class(k) <- "kernel" data(promotergene) ## train svm using custom kernel gene.k <- ksvm(Class~.,data=promotergene,kernel=k,C=10,cross=5) # works fine in this case gene.rbf <- ksvm(Class~.,data=promotergene,kernel="rbfdot",C=10,cross=5)# works fine with the rbf kernel gene.string <- ksvm(Class~.,data=promotergen...
2009 Apr 28
1
kernlab - custom kernel
hi, I am using R's "kernlab" package, exactly i am doing classification using ksvm(.) and predict.ksvm(.).I want use of custom kernel. I am getting some error. # Following R code works (with promotergene dataset): library("kernlab") s <- function(x, y) { sum((x*y)^1.25) } class(s) <- "kernel" data("promotergene") gene <- ksvm(Class ~ ., data = promotergene, kernel = s, C = 10, cross = 5) gene pred<-predict(gene, promotergene[c(6), -1]) # but the same c...
2009 Dec 25
2
Help with SVM package Kernlab
...lied only to factors with 2 or more levels The training file is a data frame with 501 columns: Col 1 is "Class" which is "+" or "-" and Cols V1 to V500 are "A/C/G/T" . There are 200 seq's for training (100 + and - each). this is very similar to the "promotergene" data set included as example with the package. The model that I have generated is as follows: modelforSVM <- ksvm(Class ~ ., data = train500, kernel = "rbfdot", kpar = "automatic", C = 60, cross = 3, prob.model = TRUE) The testSeq is a vector of 500 characters caste...
2007 Aug 08
0
ksvm-kernel
...rix (S4 method for signature 'kernelMatrix') #executing the following sentences library(kernlab) # identity kernel k <- function(x,y) { n<-length(x) cont<-0 for(i in 1:n){ if(x[i]==y[i]){ cont<-cont+1 } } cont } class(k) <- "kernel" data(promotergene) ind <- sample(1:dim(promotergene)[1],20) genetrain <- promotergene[-ind, -1] genetest <- promotergene[ind,-1 ] kx <- kernelMatrix(k, as.matrix(genetrain)) y<-as.vector(promotergene[-ind,1 ]) #y<-as.factor(promotergene[-ind,1 ]) y gene1 <- ksvm(kx, y, type="C-svc"...
2009 Oct 04
3
error installing/compiling kernlab
Hi everybody, I''m using R on a 64-bit Ubuntu 9.04 (Jaunty). I prefer to install R packages from source, even if they are available in Synaptic. The problem is that I can''t install/compile kernlab. Everything works fine until it gets to the lazy loading part: ** preparing package for lazy loading Creating a new generic function for "terms" in "kernlab"