fit: Fit a bascule object
In caravagnalab/basilica: bascule

View source: R/fit.R

fit	R Documentation

Fit a bascule object

Description

Fit a bascule object

Usage

fit(
  counts,
  k_list,
  cluster = NULL,
  reference_cat = list(SBS = COSMIC_filt, DBS = COSMIC_dbs),
  keep_sigs = c("SBS1", "SBS5"),
  hyperparameters = NULL,
  lr = 0.005,
  optim_gamma = 0.1,
  n_steps = 3000,
  py = NULL,
  enumer = "parallel",
  nonparametric = TRUE,
  autoguide = FALSE,
  filter_dn = FALSE,
  min_exposure = 0.2,
  CUDA = TRUE,
  compile = FALSE,
  store_parameters = FALSE,
  store_fits = TRUE,
  seed_list = c(10)
)

Arguments

`counts`	List of mutation counts matrices from multiple variant types.
`k_list`	List of number of denovo signatures to test.
`cluster`	Maximum number of clusters. If 'NULL', no clustering will be performed.
`reference_cat`	List of reference catalogues to use for NMF. Names must be the same as input counts.
`keep_sigs`	List of reference signatures to keep even if found with low exposures.
`hyperparameters`	List of hyperparameters passed to the NMF and clustering models.
`lr`	Learning rate used for SVI.
`optim_gamma`	Deprecated
`n_steps`	Number of iterations for inference.
`py`	User-installed version of `pybascule` package
`enumer`	Enumeration used for clustering (either 'parallel' or 'sequential').
`nonparametric`	Deprecated. The model only works in nonparametric way.
`autoguide`	Logical. If 'TRUE', the clustering model will use the Pyro autoguide.
`filter_dn`	Logical. If 'TRUE', all contexts below 0.01 in denovo signatures will be set to 0, provided the filtered signatures remain consistent with the inferred ones.
`min_exposure`	Reference signatures with an exposures lower than 'min_exposure' will be dropped.
`CUDA`	Logical. If 'TRUE' and a GPU is available, the models will run on GPU.
`compile`	Deprecated.
`store_parameters`	Logical. If 'TRUE', parameters at every step of inference will be stored in the object.
`store_fits`	Logical. If 'TRUE', all tested fits, i.e., for every value of 'K', will be stored in the object.
`seed_list`	List of seeds used for every input configuration.