- nmf_matrix
a matrix
used for NMF decomposition with rows indicate samples and columns indicate components.
- result_prefix
prefix for result data files.
- destdir
path to save data runs, default is tempdir()
.
- method
default is "L1W.L2H", which uses an exponential prior for W and
a half-normal prior for H (This method is used by PCAWG project, see reference #3).
You can also use "L1KL" to set expoential priors for both W and H, and "L2KL" to
set half-normal priors for both W and H. The latter two methods are originally
implemented by SignatureAnalyzer software.
- strategy
the selection strategy for returned data. Set 'stable' for getting optimal
result from the most frequent K. Set 'optimal' for getting optimal result from all Ks.
Set 'ms' for getting result with maximum mean cosine similarity with provided reference
signatures. See ref_sigs
option for details.
If you want select other solution, please check get_bayesian_result.
- ref_sigs
A Signature object or matrix or string for specifying
reference signatures, only used when strategy = 'ms'
.
See Signature
and sig_db
options in get_sig_similarity for details.
- K0
number of initial signatures.
- nrun
number of independent simulations.
- niter
the maximum number of iterations.
- tol
tolerance for convergence.
- cores
number of cpu cores to run NMF.
- optimize
if TRUE
, then refit the denovo signatures with QP method, see sig_fit.
- skip
if TRUE
, it will skip running a previous stored result. This can be used to
extend run times, e.g. you try running 10 times firstly and then you want to extend it to
20 times.
- recover
if TRUE
, try to recover result from previous runs based on input result_prefix
,
destdir
and nrun
. This is pretty useful for reproducing result. Please use skip
if you want
to recover an unfinished job.