what's the meaning of t and k?
crazyhottommy opened this issue · 1 comments
crazyhottommy commented
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 commented
I checked all versions and the -t option does not exist.
Best.