diff --git a/README.md b/README.md index fa6c68f..23cbf48 100644 --- a/README.md +++ b/README.md @@ -12,9 +12,9 @@ iGakco-SVM takes several parameters: Usage: ./GaKCo [options] 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) @@ -22,5 +22,5 @@ iGakco-SVM takes several parameters: 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 ```