fit: Fitting the denoising autoencoder
In FRASER: Find RAre Splicing Events in RNA-Seq Data

Description Usage Arguments Value See Also

This method corrects for confounders in the data and fits a beta-binomial distribution to the introns/splice sites.

For more details please see FRASER.

## S3 method for class 'FraserDataSet'
fit(
  object,
  implementation = c("PCA", "PCA-BB-Decoder", "AE", "AE-weighted", "PCA-BB-full",
    "fullAE", "PCA-regression", "PCA-reg-full", "PCA-BB-Decoder-no-weights", "BB"),
  q,
  type = "psi3",
  rhoRange = c(1e-08, 1 - 1e-08),
  weighted = FALSE,
  noiseAlpha = 1,
  convergence = 1e-05,
  iterations = 15,
  initialize = TRUE,
  control = list(),
  BPPARAM = bpparam(),
  nSubset = 15000,
  minDeltaPsi = 0.1,
  ...
)

`object`	A `FraserDataSet` object
`implementation`	The method that should be used to correct for confounders.
`q`	The encoding dimensions to be used during the fitting proceadure. Should be fitted using `optimHyperParams` if unknown. If a named vector is provided it is used for the different splicing types.
`type`	The type of PSI (psi5, psi3 or theta for theta/splicing efficiency)
`rhoRange`	Defines the range of values that rho parameter from the beta-binomial distribution is allowed to take. For very small values of rho, the loss can be instable, so it is not recommended to allow rho < 1e-8.
`weighted`	If TRUE, the weighted implementation of the autoencoder is used
`noiseAlpha`	Controls the amount of noise that is added for the denoising autoencoder.
`convergence`	The fit is considered to have converged if the difference between the previous and the current loss is smaller than this threshold.
`iterations`	The maximal number of iterations. When the autoencoder has not yet converged after these number of iterations, the fit stops anyway.
`initialize`	If FALSE and a fit has been previoulsy run, the values from the previous fit will be used as initial values. If TRUE, (re-)initialization will be done.
`control`	List of control parameters passed on to optim().
`BPPARAM`	the BiocParallel parameters for the parallelization
`nSubset`	The size of the subset to be used in fitting if subsetting is used.
`minDeltaPsi`	Minimal delta psi of an intron to be be considered a variable intron.
`...`	Currently not used