[BioC] use selectWeka() for feature selection

kai wang [guest] guest at bioconductor.org
Tue Nov 12 05:59:57 CET 2013


I'm trying to use selectWeka() from BioSeqClass to do feature selection. But there's an error as below:
> trainset=read.csv('D:\\7617_des.csv', header = TRUE)
> data=trainset[,1:313]
> class=trainset[,314]
> input=data.frame(data,class)
> result=selectWeka(input,evaluator=SVMAttributeEval,search="Ranker",50)
Error in paste("java -cp ", file.path(path.package("BioSeqClass"), "scripts",  : 
  object 'SVMAttributeEval' not found

How to fix it?


Kai Wang

 -- output of sessionInfo(): 

> sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-w64-mingw32/x64 (64-bit)

[1] LC_COLLATE=Chinese (Simplified)_People's Republic of China.936 
[2] LC_CTYPE=Chinese (Simplified)_People's Republic of China.936   
[3] LC_MONETARY=Chinese (Simplified)_People's Republic of China.936
[4] LC_NUMERIC=C                                                   
[5] LC_TIME=Chinese (Simplified)_People's Republic of China.936    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] BioSeqClass_1.20.0   scatterplot3d_0.3-33 BiocInstaller_1.12.0

loaded via a namespace (and not attached):
 [1] Biobase_2.22.0     BiocGenerics_0.8.0 Biostrings_2.30.0 
 [4] class_7.3-9        coin_1.0-23        e1071_1.6-1       
 [7] foreign_0.8-57     grid_3.0.2         ipred_0.9-2       
[10] IRanges_1.20.5     KernSmooth_2.23-10 klaR_0.6-9        
[13] lattice_0.20-24    MASS_7.3-29        modeltools_0.2-21 
[16] mvtnorm_0.9-9996   nnet_7.3-7         parallel_3.0.2    
[19] party_1.0-10       prodlim_1.3.7      randomForest_4.6-7
[22] rpart_4.1-3        sandwich_2.3-0     splines_3.0.2     
[25] stats4_3.0.2       strucchange_1.5-0  survival_2.37-4   
[28] tools_3.0.2        tree_1.0-34        XVector_0.2.0     
[31] zoo_1.7-10        

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