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readme.txt 2015-01-30 732 Bytes
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10Fold_CrossValidation.r 2015-01-30 9.5 kB
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Figure_3.pdf 2015-01-30 281.6 kB
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Human_train.dat 2015-01-30 954.0 kB
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Totals: 4 Items   1.2 MB 3 
Many users asked about how to generate the Two-graph ROC curve (i.e. panel D of Figure_3 in our CPAT paper: http://nar.oxfordjournals.org/content/41/6/e74.full) to determine the optimum cutoff.

Here we provide the R code and the associated data table, so that uses could exactly reproduce Figure 3 in our paper. It is fairly easy to change the R code to accommodate their own data.


Human_train.dat (20,000 rows includes 10,000 coding and 10,000 noncoding genes): 
	Column-1: gene ID
	Column-2: mRNA size
	Column-3: ORF size
	Column-4: Fickett score
	Column-5: hexamer usage
	Column-6: Label (1: coding, 0: noncoding)

Note:
	ROCR (http://cran.r-project.org/web/packages/ROCR/index.html) must be installed to run the above R code.
Source: readme.txt, updated 2015-01-30