Update README.md

README.md

@@ -12,15 +12,15 @@ iGakco-SVM takes several parameters:
         Usage: ./GaKCo [options] <trainingFile> <testingFile> <dictionaryFile> <labelsFile> <kernelFile>
           g : gmer length; length of substrings (with up to m mismatches) used to compare sequences. Constraints: 0 < g < 20
           k : kmer length; length of non-gapped substrings within gmers. Constraints: k < g
-          n : (optional) maxmimum number of examples in the dataset. Default: 15000
           t : (optional) number of threads to use. Set to 1 to not parallelize kernel computation. 
           C : (optional) SVM C parameter. Default: 1.0
+          p : (optional) Flag to generate probability of class or not. Without it, AUC can't be calculated Default is 0
           trainingFile : set of training examples in FASTA format
           testingFile : set of testing examples in FASTA format
           dictionaryFile : file containing alphabet of characters that appear in the sequences (text file)
           labelsFile : name of the file to place labels from the examples (text file). Used by iGakco to create kernel matrix
           kernelFile : where to write kernel matrix computed by iGakco (text file)
 For example:
 ```
-  $ ./GaKCo -g 7 -k 5 -n 20000 -t 4 -C 1.1 trainingSet.fasta testSet.fasta protein.dictionary.txt labelsFile.txt kernel.txt
+  $ ./GaKCo -g 7 -k 5 -p 1 -t 4 -C .01 trainingSet.fasta testSet.fasta protein.dictionary.txt labelsFile.txt kernel.txt
 ```