what's the meaning of t and k?

[crazyhottommy]

Hi,

I know k is the gene set size. if k=4, the CoMet will find set of genes of size 4. those 4 genes are mutually exclusive. could you please explain a bit on t?

python run_comet.py -h            
Note: The Multi-Dendrix Python module could not be found. Using only random initializations...
usage: run_comet.py [-h] -o OUTPUT_PREFIX [-v] [--seed SEED] -m
                    MUTATION_MATRIX [-mf MIN_FREQ] [-pf PATIENT_FILE]
                    [-gf GENE_FILE] -ks [GENE_SET_SIZES [GENE_SET_SIZES ...]]
                    [-N NUM_ITERATIONS] [-NStop N_STOP] [-s STEP_LENGTH]
                    [-init [INITIAL_SOLN [INITIAL_SOLN ...]]]
                    [-acc ACCELERATOR] [-sub SUBTYPE] [-ce CORE_EVENTS]
                    [-r NUM_INITIAL] [--exact_cut EXACT_CUT]
                    [--binom_cut BINOM_CUT] [-nt NT]
                    [-tv TOTAL_DISTANCE_CUTOFF]
                    [--precomputed_scores PRECOMPUTED_SCORES]

And now, the argument changed to -ks, but when I specify -k 4 -t 4. the program still runs without error.

-ks [GENE_SET_SIZES [GENE_SET_SIZES ...]], --gene_set_sizes [GENE_SET_SIZES [GENE_SET_SIZES ...]]
                        Gene set sizes (length must be t). This or -k must be
                        set.

Thanks for your time.

Ming

[renatopuga]

I checked all versions and the -t option does not exist.

Best.